I was buffled in the beginning as well when this happened - the simple reasons were:
a) i hit the damned bottom of the ocean
b) my hull integrity was well below 100% through enemyfire
c) i forgot to suspent silent running mode so repairs didnt start
d) i crashed into wrecks of ships i just sent to the bottom of the ocean in shallow waters
e) i hit the concretewalls of harbors not visible in mapmode
dunno if there is a logfile for it, but i doubt it

P.S. just made a custommission for checking it out
The attacking spitfires could hit my boat with their machineguns running with 8 knots 30m below the waterline taking massive damage in a few seconds starting with the rear torpedocompartment rip through the boat til it hits the front. Since successful repairs didnt last long enough the planes are adjusting their attackangle diving down attacking the dived boat. It took mostly less then 10s til i got the R.I.P. screen.