I have an interesting bug that seems to only appear when loading a lot of kerbals on a single rocket. It also might be specific to the cabin IVA I'm using.
craft file: https://www.dropbox.com/s/eky9e562le7pmqj/Space Camp Lander.craft?dl=0 requires tweakscale, Procedural Wings, and Mk2Expansion
Log file: https://www.dropbox.com/s/5f8vtnhmb7yfy3n/Player.log?dl=0
With this craft file and log file (I've tried to reduce as far as I can the number of mods for recreate) some of the kerbals get in their proper seats, and then a whole bunch load clipped through the cockpit. Note, this is demonstratable in sandbox by filling just one of the two cabins.
All installed mods (I couldn't figure out removing any more for my sample craft):
P.S. I've double checked (since that was just posted today) this breaks on the newest version, but was present on the previous version as well as I discovered the bug last night, but verified it today.