did you guys also have a buff engineer? heavy rounds in a buffed carronade can one-shot a balloon or are used for sniping guns. that was probably the captain's thinking - to sneak up on them and take them out with the heavy rounds, and keep the engineer that has the heavy rounds on the gun so they can keep shooting.
and it's already been said, the carronade doesn't have much range, so approaching probably isn't the best time to hit it.
I'd also say the carronade doesn't have a long reload time, and losing the last of the clip in the gun isn't a big deal. but giving away your ship's position if the pilot was trying to sneak up on an enemy could've been the greater reason for it (if you were approaching from behind the mobula, that's probably exactly what's going on.)
really though, if the captain were communicating with his crew more effectively, that whole situation could have been prevented. my best matches 9 times out of 10 are ones where the captains are talking to the crew constantly or divied up roles from the start.