@Redtax
I use a lot of mods, but I believe this started happening after the patch and not after installing any mod that should effect this.
I did install a few of Haelenes class mods though, but those skills were not used on any of these NPCs, and I do not see why those mods would effect the game in this way.
I believe the bug has to do with Larian changing the need for NPCs to have the correct abilities and memory slots for the skills we give them. Now you can just give them any skill and they can use it (I believe, which is what they said would be the case from release of the game).
