In the final scene with Pete and MacGyver talking, there is a man dressed in all denim with a backpack that can be seen walking on both sides of the street and crossing the street all within the same scene, depending on who the camera is focused on.
After Sam removes the distributor cap and the mercs try to start the car, the engine acts like the battery is weak, when in fact the motor should still turn over but without firing.
When MacGyver hands the video tape to Mei Jan, the close up view of the tape in her hands is a mirror image - all the text is reversed and the tape is shown spooled to the right when it should be at the left if the tape is at the beginning and ready to play.