When Kate Lafferty is trying to escape from her kidnappers, she puts the jumper cables on the window bars, walk around the "engine" and put other ends of the jumper cables on the battery. She goes back to the window and there are no jumper cables attached to the window bars.
The missile Mac Gyver is launching is at a 30 degree angle, however, in the very next shot after the launch the missile has an 85 degree angle.
In different closeups of Kate's wristwatch, the watch design changes. The watch when they're triangulating is different from the one in the next scene where they're sabotaging the missile launch.
Kate's forearm during triangulation is alternately above and underneath radio's antenna.
The "sound oscillator" uses a sub woofer speaker, and yet produces a piercing high pitched noise.
When Kate is working on the missile, she says "If I could just get this chip out"; the device she is trying to get out is not a microchip, but is in fact an 8 way DIP switch.
When Macgyver and Kate try to catch the voices of outlaws using the radios, the camera shows their watches a few moments apart.
Macgyver's watch shows 10 to 1 while Kate's watch seems to show 10 12.
Logically both watches should show at the same time.
Footage shown of the runners crossing the bridge, which is supposedly in San Francisco, is actually from New York City. You can see the twin towers of the old (destroyed on 9/11) World Trade Center in the background.
The coordinates for the missile test - N37°47' W122°30' - are supposedly for the fictional "Clinton Narrows Bridge" (footage of the Bay Bridge between San Francisco and Oakland was used for it). The coordinates given are actually in the middle of Lands End, near the Legion of Honor on the north end of the San Francisco Peninsula. The nearest bridge is the Golden Gate Bridge.
When MacGyver makes a copy of the data to floppy disk, he appears to then stuff the floppy disk into his back pocket, which would damage the disk. Someone of MacGyver's purported technical and scientific proficiency would not make such an error.
When Kate is hacking the Defense computer system for Oslow, there are several times that she hits the backspace key instead of enter.
Even assuming their setup would work as described, they would have needed to be separated by a considerable distance (at least several miles) to accurately triangulate the third position. MacGyver said his direction was at 11 o'clock and Kate said 2 o'clock; this would have meant that their two signals would have intersected just a few yards/meters in front of them.