When MacGyver is first trying to look up Teldar Systems' file on Dave Edwards, the virus is only evident in the closeup of the computer monitor. In the wide shots before and after this closeup, however, the monitor displays a normal series of text lines with no randomly changing character display pattern.
When the filming camera pans left to watch the helicopter move away from the landing area, it hits some of the tree branches and they jostle about for the next few seconds of the shot.
Obvious stunt double for Papillon when MacGyver jumps on him from the tree. His hair is fuller and a darker gray (a wig the stunt double is wearing).
The Phoenix Foundation sign is shown covered with quite a bit of snow. The Phoenix Foundation is located in Los Angeles, where accumulating snow does not fall.
When Michael is cloning the magnetic strip on Pete's security pass, he doesn't align the cards properly as had been demonstrated earlier. He places the blank card across the original, at right angles, which would not work.
MacGyver hops behind a bar with two bartenders behind it, who watch him, and do nothing to confront him like any other normal employee would do. Even when MacGyver grabs a box of cleaner and pours it all over the bar counter and they still say nothing.