During the "trial", Pete tells Frank that the information about the ambush was classified until a couple of months earlier, yet Mac later tells Michael that the information had been classified until about five months earlier, when Pete had wanted to tell Michael about it but Michael had refused to meet with his father at that time.
When Pete gets into the kidnappers' car, the rear door window is open in the close-up but closed in the long shot.
The tire marking which channel to take changes position from the time Pete and his kidnapper's pass it to when MacGyver comes upon it a few minutes later.
Even if Mac were able to trap a sufficient amount of swamp gas as shown, his trick wouldn't have worked. In order for the methane to explode it would have had to have been pressurized prior to ignition.
At about 40 minutes MacGyver stated methane is lighter than gas where he should have said methane is lighter than air.
The LAW, the weapon that looks like a miniaturized bazooka, wouldn't have blown up MacGyver's boat. That weapon is specially designed to disable a tank or other type of armored vehicle. The projectile must strike something very hard, like armored plate, in order to detonate. In case of Mac's boat, it would have simply passed through the hull and landed in the bayou bottom without detonating.
The fish-platter's flames go out a moment before Mac blows on them.
Obadiah's military-surplus motorboat is shown to be moving slowly along in all of the scenes prior to the shot of its actually being blown up, but then in this final shot of the explosion, the boat is motionless and does not sway or bounce at all when it detonates; it just sits solidly in the center of the stream, obviously indicating that it is mounted on a stationary base that is hidden under the water.
When MacGyver is trailing the Jeep his radio receiver indicates that the Jeep is behind him, but the Jeep is approaching MacGyver's position from ahead of him, confirmed by MacGyver's spoken narration.
Mac tells Michael that, "methane is lighter than gas, so it will push the air up out of the tube, and the tube will fill up with the gas." But he should have said that methane is lighter than AIR, and so the gas will push the air out.
While they are collecting the methane gas MacGyver says that methane has a smell. He seemed to have forgotten that natural methane has no smell. If there were a smell, it would be from the decaying matter from the swamp water, not methane.