They landed on fumes (literally-they had only SEVEN GALLONS of gasoline left!) on Okinawa, there were communication SNAFUs, nearly everything.
Check out this account here:
LINK: Near Failure at Nagasaki-The first atomic mission was executed perfectly. On the second one, almost everything went wrong.
My understanding was weight was an issue and the Enola gay came back with half of the fuel they left with .