Got just the same issue. Version 1.5.1.712, both DLCs installed. Playing on Supernova.
Did the following:
After completing "By His Bootstraps" quest told Anton that his dream of Byzantium is meaningless (lines with Persuade check)
Negotiated peaceful conclusion for guards and outlaws
Killed 3/12 raptidons, sedated the rest of them
Convinced Cassandra to hand over the research
Guess, I should replay a decent part of the Roseway story and resolve the quest in a different way, which will not fit my current character. It's a shame.
Although, did all the players here encountered the bug after killing (at least several) raptidons in the lab? Maybe with 0/12 the quest resolves correctly?
UPD: Tried to proceed with the quest a little different, but with the same outcome (negotiated peace, Cassandra handed over the research). Killed 0/12 raptidons this time, tried both options with the security keycard to open the fence. Nothing changed, the issue still persists. For now I decided to postpone the walkthrough until the issue will be resolved. Captain Janeway don't like other outcomes in a least. I also sent a ticket to Private Division. I hope they'll respond, 'cause support on this forum seems dead to me.
UPD2: Got an answer from the Private Division support team. They confirmed the bug after receiving my save data and forwarded the issue to the QA team. Lets us hope for resolving it in near future.
