What was probably hitting the water was rounds and/or shell casings from the "mad minute" (probably longer) of the other boats laying in suppressive fire onto the shore. From under the water, one would be hard pressed to tell where the rounds were coming from. If it had been an ambush, there almost certainly would have been motar and/or RPG rounds coming as well as small arms. If it was a command detonated mine, as opposed to one set off by a tripwire or pressure switch or someother mechanism, I suspect whoever detonated the mine was too busy diddy-bopping out of there to be shooting at the boats.
Any bullet holes in the boats?? "If there ain't no holes, there weren't no FOES".