Factual error: A 250-year-old sea chest recovered from the ocean floor is opened, and all its paper items are perfectly dry: the log book can be opened and read, and the letters can easily be unrolled. Highly unlikely. The chest's wood and pitch would deteriorate (salt water is extremely corrosive), and the paper should be damp and crumbly, at the very least. Even more likely, it would have become a lump of unreadable sludge.

Continuity: During the car chase through the desert, the rear view mirrors on both cars disappear and reappear repeatedly.

Audio problem: At night when MacGyver and Jack are sneaking past the guards behind a mule, we see about 8 to 10 light bulbs hanging overhead. MacGyver later pulls the cord down and all the lights begin to pop. There are about 16 pops, many more than there were bulbs on the cord.

Continuity: When MacGyver et al. spot the car they will use to escape, the headlights are clean and white. After the commercial break, they are much dirtier and the dirt is only on certain precise spots on the headlights.