I have recently had problems with stellaris crashing over 3 seperate playthroughs with acot, overrides and sofe enabled. I have now found the cause of the crash, and that is because of what i can only assume to be a bug with the giga fortress building or Virtual Strike decision as both where present on a habitat with around 30 000 ground forces (not strength but actuall number), which persisted even after all jobs that provided forces where disabled (dark enforcers, giga cannon operators, etc). Removing the colony through commands did remove the armies and allowed me to avoid the constant crashing, but it did take me over 4 days to find this bug and 3 playthroughs which almost had me quitting the game entirely.
Just thought that this bug should be known as it was very annoying if one does not know how to fix it and it happen consistently for me around ingame year 2360 - 2380.