Well, for the bats the reason is: I keep forgetting to do it since the complains about that one aren't as frequent; I'm already adding one for that as well as debugging the skip for the guards. For now maybe save scumming can help until I add the skip, but then again: Sorry for the inconvenience.
Glad to see you're enjoying everything else, I'm already working on a overhaul for the game's code so this and other issues with it don't happen anymore (but that one will take some time...), for now I'll have to patch it, so thanks for letting me know!