Finished the run after some interruptions, and noticed two peculiarities:
1) I saved and quit during the flagship fight and when I resumed the game, the hacked missiles room was still locked, but wouldn't open if I removed all power from hacking. On the screen, it was indicated that the beam room was hacked instead - but still, enemy crew had to break open the door to the missile room to enter. I think I've seen this before, so it may not be a new bug.
2) It was the first game of the new profile, but when I came to the stats page, three ships were listed in the top ships, only won with a victory sign. However, the stats showed 1 victory in 1 game played. Since I stress-tested the game by just closing the window two times during play (this would sometimes delete the profile in previous versions), I think the two phantom ships on the stats page were generated when I just closed the game window. I think this is a new bug, I haven't noticed it in previous versions.