I ran into the same bug. It would happen if I went into Gareth's room after the flashback cut scene with Zakhar and Gareth, and the conversion with Zakhar. Zakhar would come after me to kill me, like he does in the "bring him" path, but regardless of what I'd done beforehand in between the cut scenes and Gareth's room. The only way I got around it was going into his room before seeing the secret room with Zakhar.