7 years into my fort and I'v noticed some rather odd bugs.
Mindless dead will not attack invaders. Nor will invaders attack them. This also includes my own skeletons that get stuck outside of the fort and I lose control of. They will only go after wild animals. They won't even attack animal mounts. I had a small army of animated corpses from the necromatic circle path *through* the invading army just to kill monkeys. I suspect invaders are receiving the same syndrome buff that warlocks receive.
Cannot appoint a cryptlord. (I think this one is known).
Skeletons that are in the military, do not stay in the military. Even surrounded by pylons and warlocks, they still disappear from the cryptlord squad I stick them in. I used therapists assign unit to military function as a workaround for inability to appoint a cryptlord noble. (They pop out of the squad within 1 - 5 minutes. I never lost control of them). Interestingly enough, they tend to hold onto their equipment even though they aren't in the military. My ironbone skeleton archers, JFK and Elvis will shoot at any enemy that wanders to close despite no longer being in a squad.
I have a theory. It is only based on how I think I understand how you made all this work. I suspect it has to do with the overlapping syndrome buff that keeps them controllable. Even though they are controllable, the act up updating the state of the skeleton from when one buff wears out and a new one is applied does it. If this is the case, then I also suspect building the skeleton banner will fix it, since then there will no longer be a state change. I'm a hellava long way from testing that theory.
Torture Chamber: I've been having lots of fun using this one on the random things that invade me. A were-dwarf-gilla monster got stuck in my cage traps. I turned him into a ghoul. However, this doesn't cure the were monster curse, and he transformed and attacked later. (Not really a bug, I was just curious how they would interact). However, all my ghouls created from invaders get attacked by some members of my fort and killed. I turned a number of goblins into ghouls, and my own skeletons beat them to death. Not sure why. I'm assuming it has to do with the invader performing a hostile action while in life and thus is still viewed as hostile as a ghoul.
Fort wealth. My wealth has overflowed into the negative integers....then magically became positive normal wealth numbers later. I don't mind, except it has my fort a free for all for invasions despite being nowhere near the population requirements. I had my first invasion before I hit 20 civ members. Now I'm at 34 and I have massive 100 man armies of dwarves, drow, orcs, and goblins beating down my door at all times.