Are you playing with the Blue Sun mod? If you do, it might be caused by an issue I've been trying to fix the last couple of days. It has to do with a mix-up of GUMID's and it's a hard one to find. But it will be fixed in the final release.
I'll look into the Bernice issue as well. It prolly has to do with how the source code finishes the mission. It should be easy to fix with a simple replace function.
If you're playing with vanilla there might be an error in one of the ini files that makes the mercs unrecognizable by the game engine.
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