Either you had a maintenance failure take out some of the life support (crew quarters) or the ship was designed without enough crew quarters, which shouldn't be possible since they're automatically added, or else you overloaded the ships life support by picking up a life boat.
The first option is most likely, engineering spaces lower a ships chance of maintenance failure, and if the ship has enough MSP to cover the repair cost of the failed component it will be automatically repaired with the appropiate amount of MSP removed from its storage.
