I'm having the same exact problem. I haven't been able to figure out what causes it. I'm in my friend's hosted game, and it seems about 60-70% of the time we reload a save, all the skills are gone from the skillbars on both characters. As stated with an incarnate, it spawns with no skills, not even a basic attack in the hotbar. Even when we do reload and the skills are there, the incarnate still spawns with no skills. We're at a part in the story where we've gotten a 5th person to follow a party member. In combat. they have no skills either as long as I'm controlling them.
I don't know if it's related, but I also had trouble removing skills from my character's loadout in the skill menu. whenever I got rid of contaminate, it came right back, until I was quick enough to remove and replace it before it popped back.
We've both restarted our computers to no avail