Thanks for your fast answer!
I tried it with the barbarian from the dungeon pack, but I already had the problem with PrototypePete.
I think they do it on every animation. There's always at least on point, where both arms snap out of place.
But: I just tried it in Godot 3.2.3 and that actually fixed the problem. I imported the file in 3.2.3 and saved it as a scene, then I opened it in 3.3 and it worked just fine. I don't know why this issue occurs, but at least there's a workaround. :)
Sorry for taking up your time and thanks for your help!