Found a few bugs, only one of which (the one that kicks you back to main menu if you trigger it a couple of times) is particularly noteworthy. As before, I tried to narrow down the actual script line causing it when I could.
moods.rpy 231: (consulting your notes)
Selecting the notes on Alice also gets you the notes on Beau. Looks like a missing 'return' between the two.
morning.rpy 435: (Landing pad, morning)
Selecting "Say goodbye" when talking to Rachel hits a 'return' statment that was reached without a corresponding 'call'. Player gets dumped to the last unused location in the return stack, or kicked to the main menu if the return stack is empty. Could probably be fixed by replacing the 'return' with a 'jump morningDock'
morning.rpy 629 and 658: (Hunter's room, day)
These two sections use the old background art (bg roomhunter instead of bg roomhunter day), so the hole in the wall appears to change dramatically in size between day and night.
script.rpy 181: (map screen)
Selecting Factory and then cancelling out of the map screen takes you to the garden. Swapping "call .start from _call_map_start_2" with "jump .start" _should_ fix it, but I haven't tested that.
tutorialscenes.rpy 313 and 329: (welcome party; the "Tape? Tape." segment)
Not sure if two copies of the welcome wallflowers panel are meant to be visible at the same time. Could be a bug, could be my brain being weird about it.