Welcome to the forums, Mantis 
You have run into a common and very irritating bug that Funcom is aware of, and, hopefully, trying to fix. There are a few things you can do to prevent it.
First, never have two weapons in a thrall’s inventory during a fight; they aren’t too smart and it confuses them. There is one exception.
To equip a thrall, I put them on guard in a base, then give them a weapon and a truncheon, and a piece of steak for the buff, BTW. When I get to the area and see whether or not I want to knock them out, I remove the one that I do not want them to use. Until in a place where I can place them on guard, I never change weapons. This practice works most of the time. I also test them out on a trivial enemy before entering a dungeon or the Unnamed City, for instance.
If you find you are out in the wild and that happens, there are a few workarounds that might work, but are a bit complicated and somewhat dangerous, so I pull them away far enough to repeat the above process and see if it works. If not, I change thralls and start again.
Good luck !
Regards
jim