I've seen the same thing. Mine tend to remember the skills I give them, but any skills I removed always pop back in. Tried to make a ranger/rogue type character, taken from a rogue pre-build - ditched the majority of the scoundrel skills and gave it a few huntsman skills for a bit of balance between range and melee. Next time I load up the editor, he has the huntsman skills I gave him, plus all the scoundrel skills he started with. Annoyingly, I gave him the same scoundrel skill again by accident, so when I load it, he has two copies (he can use both as they have their own cooldowns).
I have a sticky set aside for him and one of his mates to remind me to remove the skills every time I load the campaign. Bit of a nuisance. Hopefully it'll get patched.
