The main culprit *seems* to be the PEC and Crew Quarters.
My save corrupted due to me saving in Crew Quarters. I guess it was my fault although I have read that it's not wise saving on puzzle rooms... but that time I was so sleepy and not thinking straight I guess........
I haven't saved in any of the puzzle rooms but I passed the crew quarters with no crashing. I've mostly just been closing the 3ds in general when I feel like stopping which has been in puzzle rooms a lot.
It's not really your fault, it's pretty shitty that I need to always be aware of when I shouldn't be saving. As much as I'm enjoying the game, if I lost the 13 hours of progress I have, I would not be trying it again.