Re: What caused the missile SNAFU: no clue. Never seen any bug like that before. Here's how to fix it:
1. Figure out how many you made. Multiply that by the resource cost. Then, follow this menu path:
A) Main game bar: Spacemaster -> Spacemaster On
B) Main game bar/System display window/whatever: Open Economics window (F2) -> First tab (Summary), select Earth (this should be selected by default, but just in case) -> SM Mods button (bottom-right) -> Go to each of the relevant boxes for the missing minerals. Add the missing total to whatever sum is already there. That's your total mined stockpile on Earth, so once you've added the appropriate minerals back you're good to go on that front.
2. Design a completely new missile. Maybe you did add the sensor accidentally, maybe the design bugged out somehow, it doesn't really matter. Use the Instant RST button in the Research tab to research it instantly instead of starting a new project to research it; it's only fair, given that you've already spent time and wealth researching the design once.
3. Build a test run of the new missile, make sure it's set up properly.
4. Go to your stockpiles (Stockpiles button, upper-right of Industry tab), scrap the missiles. It'll give you extra resources back, but you can consider that payment for the waste of time. Or just let them sit there forever being an eyesore. :V
Re: the ships:
Calgary:
-The beam FCs have 60% tracking speed over the turrets. Unless you just have disproportionately high FC tracking speed tech, you're either wasting volume (by not matching them to the turrets) or TS (by not making the turrets as fast as the FCs).
-One reactor is kinda chancy. All it takes is one unfortunate hit to put your lasers out of action. Same deal here as with fuel tanks and drives: it's almost always better to have multiple smaller ones rather than one big one, so that taking damage to them just reduces your capabilities instead of ruining them.
-The active sensor resolution is way too high if you're not going to always operate these alongside dedicated sensor ships. >=5000t at max range is okay for high-tech warships which have maximum active ranges in excess of 500+m km (and thus a much wider buffer for the >=1000t range), but not for this. FACs will be able to get pretty close before you see them, and depending on the size of the missiles you run into you might not see them at all (though you're using CIWS as your main PD, so that's less of an issue).
Saskatoon:
-Deployment time is still set to 3 months.
-It looks like those reactors provide five times the power that you need to keep up your maximum rate of fire.
-No active sensor at all. If your sensor ships go down, these are useless.
Both:
-Heavily limited range. They'll do fine for defending Sol, but anything more than one system away and you're not going to have the fuel to get out, maneuver in combat, and make it back.
I'd also question relying on CIWS for PD. That's pretty much only appropriate for commercial vessels, ships which will spend the vast majority of their time operating alone, and as supplementary defense for capital ships. This is because CIWS, unlike all other types of PD, can only defend the ship it's mounted on. Generally even using the same tonnage for gauss turrets, FCs, and res-1 actives is going to be more effective for groups.
For the Calgary, I'd recommend trimming the magazine space down to ~20 salvos worth of missiles and using the tonnage for a better active sensor, more fuel, as well as swapping out the CIWS for laser or gauss PD.
For the Saskatoon, I'd recommend fixing the deployment time, adding an active sensor for the main turrets, swapping the CIWS for laser or gauss PD, adding an anti-missile active, and adding more fuel. This one can afford to take on some extra tonnage anyways, since it's ~1k km/s faster than the Calgary; you're never going to use that extra speed unless all the missile boats die.