It was the final encounter today, with the Hydra boss from the Final Shape campaign mission, and the team ran ahead leading to me Joining Allies. This then put me in a black screen, with audio, where I could do nothing while they did the fight. I assume if they whipped that we would have fully reset and I would have been freed. Regardless, I don't know, and do not plan to replicate, if this is affecting any other encounters. After they defeated the boss, I was pulled to the next location for rewards.