When MacGyver is disarming the second bomb, exterior shots looking into the bomb show his improvised vacuum sucking phosphorous from the dish, but interior shots looking out of the bomb at MacGyver show the dish of phosphorous untouched.
As the camera pans over Venice Beach towards MacGyver's apartment, MacGyver's voice-over says there's nothing he likes better then a sunny day. Yet the sky is overcast/cloudy and as the camera pans to MacGyver on his balcony, he's completely shaded. The camera then cuts to a close-up of Mac, and he's now in sunlight.
When Charlie breaks the vacuum of the bomb case, the pile of yellow powder disperses into the air. The camera angle changes and the pile of powder is back in the dish again just before the bomb explodes.
When moving from the balcony to his apartment's interior, MacGyver's shirt changes color.
The phosphorus in the dish is yellow, yet when Carole starts to insert the neon tube into the bomb's seal, the dish has black powder in it.
The vacuum tube would not be able to suck out the powder because the bomb's chamber was itself a vacuum, so there would be no interior pressure to push the powder into the tube.
The supposed footage of Midway really isn't Midway. The stock footage of the island shown is large and wooded. Midway is a tiny barren atoll with very little vegetation.
The needle that Charlie inserts into the gasket is just lightly coated with Vaseline, and most of it would have been wiped off anyway as the needle was slid into the pierced hole, so there would not have been enough grease present to create the huge continuous bluish plume shown when the vacuum was broken.
When MacGyver is inserting the vacuum tube he tells Carol that the silicon around the tube creates an air-tight seal which allows them to vacuum the phosphorous. Mac inserts his tube too close to the glass and you can see it creates a U-shape tear which wouldn't be air-tight.
Mac speaks of his landlady as "Susan", yet the end credits identify her as "Suzanne". She was also listed as Susan in the previous episode.
When Pete shows Charlie and MacGyver the location of the Victoria to Typhoon Harry, the silhouette of the storm is more reminiscent of a tornado rather than a tropical cyclone.
For a second you can see what may be part of the airplane the filming crew is in, filming the small plane MacGyver and Charlie are in, in the top of the screen.
Pete, when briefing MacGyver and Charlie, indicates on the map the ship is somewhere near the Kamchatka Peninsula (off Russia). Yet the Lat,/Long. co-ordinates given in the opening sequence show the ship about the Lat. of San Francisco and a fair way east of the international dateline. Quite some thousands of miles from the map indication.