The NCIS/OSP team swim underwater to the boathouse and enter it from beneath, via a hatch in the floor. However, apart from one pair of wet fins, they are all completely dry.
When the four bad guys arrive at the boat shed, Deeks says that they're wearing body armor and are loaded for bear. Three of the bad guys are taken down with just 2 or 3 bullets from pistols each. If they were wearing body armor they would have needed to be shot in the head to be killed so quickly. But when the agents removed their masks there was no sign of damage or blood on their heads or faces, and there was no sign of blood on the floor beneath their heads.
During the drive-by shooting one of the bullets hits the tire of Deeks' pickup but it stays inflated, the bullet holes are clearly CGI. Plus they are way too large to be from the .30 caliber AK-47 the shooter used, they look like the size of a .50 caliber bullet hole.