Stack trace:

    @   000007FEEBC343C5  	principia__GetPlottingFrame [0x000007FEEBC343C4+230920]
    @   000007FEEBB9F13B  	principia__FlightPlanCreate [0x000007FEEBB9F13A+572970]
    @   000007FEEBBF5744  	principia__LogFatal [0x000007FEEBBF5743+111]
    @   000000013F363F0D  	(No symbol) [0x000000013F363F0C]
F1104 20:43:12.629523  1628 interface.cpp:668] System.NullReferenceException: 

  at (wrapper managed-to-native) UnityEngine.Component:get_gameObject ()

  at principia.ksp_plugin_adapter.PrincipiaPluginAdapter+<AdvanceAndNudgeVesselsAfterPhysicsSimulation>d__105.MoveNext () [0x00000] in <filename unknown>:0 

So this is an exception somewhere in the WaitForFixedUpdate block. This usually hard to track, fortunately we have one level of managed stack, which tells us we are getting the gameObject property.
That seems to narrow it down to either reference to collider.gameObject.
There is a null check before the second one (which was added to fix the very similar #1447), but the first one was added (in Chasles) before that null check; moving it down should resolve this issue.

Moving it down? SOrry I don't understand much, was just trying to help, but I keep having CTDs in situations like EVA trying to enter cockpits, or transitions between surface and space...

The above was a note to ourselves, describing what we need to do to solve this issue. No action is required on your part.

OK, Here I have more logs in case it is helpful. This time tying to enter my cabin in space near mun.
https://www.dropbox.com/s/yn3i35y8vkhn4cj/Principia.rar?dl=0
https://www.dropbox.com/s/t3h8pmwg4fvvz3x/KSP.log?dl=0
Also a KSP crash log https://www.dropbox.com/s/ljpsx4qdpw4iath/output_log.txt?dl=0
I reloaded the game and can't get inside my cabin(It keeps crashing) I really don't want to lose this vessel... :(

Probably the same bug. The vessel on which the crash happened was Polar Mun Lander. Can't reproduce the bug on demand though. Adding these logs and save file just in case they are useful.
bug_report.zip