So I've noticed a personal list of things that could screw you over if you don't know them in advance in WoTC. Some of these aren't technically glitches, some of these might be in the base game, and some of them might just be my imagination. Hopefully it will help someone. Anyway, shit to know:
1. Upgrading a soldier via the training center is never free, even if the perk would be free from the promotion screen.
2. Using the "free up weapons" button will not just remove unique items, it will also remove upgraded weapons to be freed for everyone else. It can be difficult to remember who has which gun or why.
3. Some new Xcom stuff sometimes straight up don't do anything, or work differently than you expect:
3a. Interrupt does nothing. Battlelord works kind of but I've been told its totally useless.
3b. Spotter does something but its not clear what. Both bonded soldiers have to shoot the same target. Simply standing next to each other makes the bonus stronger, but still does nothing unless the other member of the pair has already shot the target.
3c. Unlocking the ripjack for normal melee attacks has a cooldown, but dash attacks only consume one action. You still need to have two actions to perform them tho.
3d. Implacable tacks an extra move-only move at the end of your turn, but that move is still lost by any "end turn" action. Run and gun still allows a wide variety of moves including bond support abilities, grenades, overwatch and reloads. Run and gun is specifically coded to NOT work with many high level Xcom abilities like Colonel. You can still move and use serial normally however.
3e. Ammo applies all effects including debuffs to more than you would expect, including templar blade attacks. It also works with ripjack, sword, and pistol attacks, even bladestorm and faceoff. Bluescreen adds a lot of flat damage and is thus crazy with low damage weapons.
3f. Remote detonation works, but trust me when I say that it NEVER comes up. Something about the map design or AI seems to separate enemies and explosives. Banish works as intended albeit as a one time consumable. However, annihilate does nothing, it is functionally identical to banish. Its unlisted, but reapers have a 0% chance to reveal on shot if no one is left alive to see them; this includes if killing an enemy frees a mind controlled/animated/shadowbound unit that could otherwise see the reaper.
3g. At least one tooltip for the templars claims they can use rend if adjacent to an enemy even if they've ended their turn on moves or pistol fires. This is a straight up lie, rend is used exactly like ranger melee.
3h. Parry blocks fucking everything, even some psi attacks. Deflection and reflection are passive and totally seperate from parry.
3i. Templar's blades are their primaries and can't be modified. However reapers and skirmishers CAN mod their weapons, with some really powerful synergy.
3j. The templar's feedback order will cause skirmishers to clone during the aliens turn and the clone will always shoot from wherever it ended up, even if flanking. The templar's "random bonuses on squadmate death" order may or may not actually do anything, I've seen no evidence that it does...
3k. Second level bond allows the removal of mental effects ONLY by ending a move next to the effected bondmate. That means if you move next to a dazed ally, you'll cure daze automatically but you won't cure the resulting disorientation unless you take another move and end up next to them. And it has to be a move, none of this shooting nonsense.
4. Some alien stuff also doesn't work like you'd think.
4a. If you're wondering what's a robot, fucking everything is a robot. Apparently even spectres and gatekeepers are robots for purposes of bluescreen rounds, but IIRC not for haywire.
4b. Purifiers are supposed to do 3 damage on hit in addition to burning, but they only cause burning and their accuracy is horrible. Additionally, environmental fires almost never cause burns, they're far more likely to cause falling damage. Purifiers also have a fire grenade that is much better than the rest of their kit, but due to its low radius the AI almost never uses it.
4c. Andromedons can break some WoTC only staircases by climbing them. If they move past the staircase they teleport to the end of their move, if they end on it they ragdall and take fall damage. Sectopods can and will instakill turrets by moving through them or firing the wrath canon past them.
4d. Shadowbound units can be rescued by killing their clone or the spectre. They can also be rescued with revival protocol, but that doesn't kill the shadow (which raises so many questions). Spectres also have a health stealing melee attack that AFAIK the AI never uses.
4e. Killing sectoids not only frees units from mind control, it also frees them from psi panic. As does flashbang. Killing chosen or allowing them to escape with a scan/captured soldier, will undo all the dazes (not sure if it cures the disorientation or grants back the lost AP).
4f. The AI seems to have a 100% chance of using its mostly harmless psi abilties rather than potent beam weapons, downgraded to maybe a coin flip if it has an easy flank. This does not seem as much of a hard and fast rule on legendary.
4g. The gatekeeper's gate ability will raise lost as psi zombies. Lost corpses never despawn, and killing reanimated lost is NOT a free action. The first action of the first gatekeeper encountered in my WoTC caimpaign saw 20 psi zombies raised, the VIP 3 stories above me killed, and 5 soldiers wounded. The gatekeeper's psi attacks (or gate, at the very least) automatically give phobias. This bypasses the normal phobia mechanics completely, has no message or chance to resist, and a single use of gate can and will give an identical phobia to the entire squad. Fortunately a colonel with no will depletion is almost immune to the effects of fears.
4h. Lost have no special ability to climb or displace Xcom soldiers. As far as I can tell, if you block a ladder they'll gather around the bottom even if they have other useful things to do;
AFAIK some positions make immune to lost.
4i. Advent priests lose all active psi effects (mind control included) if they use sustain, however they come out of stasis at the start of the alien turn with full AP. They will trigger overwatch to get back to cover before resuming the fight, alternately any DoT will kill them the moment they leave stasis. I believe that bluescreen rounds and EMP also damage holy warrior shields, even tho the barriers are presumably sci-fi magic or whatever.
4j. The warlock has a self stasis ability. It DOES cancel mind control; however it doesn't seem to be possible to cancel his MC via flashbang.
4k. The chosen weapons are solid, except the hunter's rifle, which is obscene. It has an unlisted ability that let's you move and shoot like a standard weapon, including perks.
5. Tiredness and will are the same thing, with will being the sole stat used to resist psi and panic. So yeah, will can be very important, but it has no other effects besides mental defense and tiredness/exhaustion. Psi stat for abilities is its own thing unrelated to either mechanic. If you didn't get the memo, panic works completely differently in the new game; it can apply for more than one turn, but it can only be triggered by bondmate death, severe will depletion, seeing an enemy they're afraid of, or psi attacks.
6. Resistance soldiers have seperate rules than you. They can't miss or almost can't miss, and their HP and weapon damage seems to very mildly scale with time despite their tech and abilities being the same. If you don't trigger alien pods, the resistance soldiers won't even if they shoot them; so resistance soldiers will fire all their shots on the aliens, and then the aliens will take their one or two shots at the civies.
7. The GTS and training school do almost nothing for the first month, and are pretty weak even after that. The ring on the other hand is more valuable than it might seem, covert ops give all the benefits of combat including promotions and level ups, at basically 0 risk.
8. On all difficulties, advent units will almost never crit you if you're in cover, and their base damage is bad. Its not intuitive, but being on opposite sides of the same trashcan is FAR better than being flanked.
9. The effects of destruction may or may not have been enhanced. Some (all?) ladders and staircases can be destroyed, and roof tiles will often be destroyed causing fall damage. This may just be the fact that purifiers are causing me to notice this more often however.
10. Fighting chosen stops explicit timers, even if you make objective progress during the fight. However it doesn't stop aliens from targeting civilians or VIPs. Two of the three chosen have abilities usuable without being revealed. This does not start round timers or reveal the chosen, which means they will not use their normal combat abilities until you reveal them.
10a. If chosen get access to a dazed soldier to capture or mindread them, they exit the map, which is the same as killing them except with no AP or experience rewards and a high likeliness of at least one soldier getting a phobia.
10b. Chosen strengths and weaknesses are random, except that one of their weaknesses is always enemy: X. The actual chosen abilities, however, are all present from the start. It might not seem so since some abilities (like standard shots) are quite rare, but for example the assassin actually has a certain DBZ anime attack right from square one.
11. Covert ops are refreshed every supply drop, and remain available the whole time.
12. Supply raids can be abandoned with 0 consequences. There's nothing to stop you from grabbing one or two crates and getting out of dodge, or sending in the B team for a couple cheap kills then run away.
12a. Guerilla and resistance actions can be abandoned with objective completion and the mission will be listed as a failure, but actually be mostly successful. Between the different objective types it doesn't seem 100% consistent what happens; you shouldn't lose a region, you probably cancel the dark event if there is one, and you may or may not get the listed rewards. Usuallyyyyy you get all the non-optional victory rewards but I wouldn't bet anything on that.
13. You can replace dead hero units. Under the advanced start options you can choose to start with a hero unit; this seems to be more of a standard start option rather than a "second wave" option, it has relatively little effect on game balance and the effects are mostly positive. Whichever faction you select, you should eventually get an option to recruit a second hero unit, and if you fall under two you might eventually be able to recruit more for that faction. If you didn't explicitly chose a faction, it defaults to reapers.
14. The reaper excavation order and skirmisher base bonus fully multiply with with everything including each other (so a 2x boost + a 2x boost equals 4x as fast). This isn't true of everything in the strategic game, for example research is far less generous.