I just did Mindscape on my temporal agent. When I finished it and accepted the prompted beamout, it dumped me back in the Delta Quadrant, wiped my progress in the mission, and popped up the interaction button to start it. See the linked screenshot to see how I got to the end of the mission and yet it's as if I never began it, much less completed it.
I've done it several times before. I wasn't interested in seeing it again, but it's on the list for temporal agent rewards, so I spent half an hour trudging through it... and it didn't count. I'm not pleased about that.
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There are actually similar issues on some other missions, but they're harder to cause this glitch - i just know i used to get it all the time in Everything Old is New, because I was speedrunning the mission (at the time, the phaser beam array sold for around 300,000 while a master key was only like three million, so doing a fast mission for easy money was still worthwhile.