Commander Nelson (Steven M. Gagnon) states that the bad guys' ketch can only reach "nine knots per hour". A navy commander would know that a knot is a measure of speed, one nautical mile (1.15 land miles) per hour and would quote the speed as "nine knots" and never refer to "knots per hour".
Commander Nelson is wearing an 8-sided Marine Corps cover(hat)rather than a navy one.
When MacGyver gets to the island and takes off the part of the scuba suit covering his head his hair is wet. The next scene when he's in street clothes they are dry as well a his hair. It would've been impossible for him to wear any clothes especially sneakers under the scuba suit to begin with.