Why do model swaps heads/faces get messed up in cutscenes.

So when ever i get install a mod that swaps a character model from the the game itself like if i want to play josh, barry, rebecca, etc. or if i get a model from another game like leon, claire, etc. Modder Johny Valentine has a Classic claire over sheva mod and its perfectly fine in game then in cutscenes it makes her look like a female Jeff the killer. I asked him in his thread and just said "it is beyond my power" and I would like to know why and here is a couple guesses but im not sure if i'm right. Is it because the cutscene is scripted and its special animations only affect the face and the texture gets messed up that way or is it a different texture in cutscenes and it tries to read the model swap but and cant and if you change anything in the game files it would either mess it up even more or you cant change it at all? Please tell if I'm right or not because I would like to know why every model swap mod does that.