Fliers are notoriously buggy, and yes, critters can camp in place for no apparent reason, as well as refuse to go into the fortress.
Regardless, building destroyers aren't completely bugged out, but there's no reason to assume any of the bugs witnessed for years have been dealt with either.
Edit: Well, I've contained an FB who didn't care about my juicy bait door, but eventually managed to get it locked in an airlock with the door by locking and unlocking the door to block/create a path into the fortress. The critter paces back and forth, but doesn't care about the door, regardless of whether it's locked or unlocked. I used DFHack to check the raws for it, and it is set to be a building destroyer type 2, as it should be, but apparently it doesn't know that.
I had another FB that ignored another bait door, although that might be explained by juicier live targets to chase (actually I had two, but both were eventually killed by cavern critters [I think, but I can't see the whole cavern]). I also had an undead cave ogre (slayer of one of the FBs) who just stood about 10 tiles from the bait door doing nothing until I provided a path into the fortress, at which it lumbered towards it, getting caught in a cage trap before reaching it. I thought undead building destroyers would retain that ability.
Thus, it does seem something has been broken, at least partially.