The FireStorm aircraft is shown as an F-4 Phantom II, which has a crew of 2. However, in the cockpit segments, the configuration is that of a single-seat fighter.
When attempting to repair the containment seal, MacGyver uses a Bunsen burner incorrectly with just a yellow flame. However the closeup shots show correct usage with a blue flame. This is both a character error and a continuity error in one.
When seal integrity is compromised, MacGyver looks through a microscope and says the organism is mutating. However, what you see is simple mitosis. It's not mutating, it's simply growing.
A transformer would not increase the speed of the elevator. Motor speed is determined by power line frequency and not voltage which would be boosted with the transformer.
When MacGyver removes the control panel from the wall for the the elevator, he only removes one screw even though four screws are visible (one in each corner).
After MacGyver goes through the decontamination process, where the outer layer of his skin is supposedly burned off, there is no change in the appearance of his skin or his hair.
It isn't clear what the purpose of the air strike was for. There was one plane in use which would have destroyed the area around the landing site of the crashed satellite. But there were numerous instances of dead animals spread all around the area, indicating that the deadly organism had already begun to spread out into the larger population, which should have meant the need of a large number of planes to bomb a much larger area.
It makes no sense to close sections of the facility off prior to self destruct; this would impede destruction. If complete self destruction is the aim, then this is better achieved by having all sections open to each other and not isolated.