This is an ongoing problem for a long time, The only save is for sci captains that can hit some of their abilities to decloak when it happens, unfortunately tacticals, and engineers don't have any that I have found so far to decloak the ship. If you fly close to the opponents some of their abilities will also decloak you.
Yep been broken for years, no idea why they can't or won't fix this most annoying of bugs as it affects almost everyone and can be a real mission breaker, making you have to restart the mission from scratch
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