When James Grant gives Diana Kingman the soda streamer, the level of liquid in the bottle changes, as it goes from ¾ to full. In addition, the level of milk in Mac's changes also.
When MacGyver throws his boot on top of the train to distract the bad guy he's then seen running up the stairs in just his white socks. After he's been hit and is on the floor he's seen wearing both boots again.
Near the beginning when MacGyver is being chased by the two bandits, he sets the top of the train on fire to get rid of them. After the two bandits jump off, Mac proceeds to the front of the train to talk to the conductor. He makes no attempt to put out the fire and acts like nothing has happened.