If you try to apply again does this still happen? The only thing applying does is schedule something called a "drama node" which shouldn't be capable of doing that. You may need to repair your game if its been a while.
Edit: someone below in the comments had the same problem and it turned out to be a piece of CC they installed that was causing errors when new aliens (in this case, infiltrator career coworkers) spawned in-game, you may be able to ask them what it was. If it happens consistently it's probably a default replacement of some kind.