It is calculating how many hours you flew that day, but if the crewed aircraft would reach a state that it can no longer be operated (the limit for my experience is when a vital component reaches 1% health), then it stops at that time.
Other bugs might also play a role, I had problems with changing aircraft and using crewed aircraft, however others reported that it worked for them fine, which tells me that these are fairly random bugs, none the less they might happen.