Factual error: They're in Malaysia where cars are right-hand drive, and they drive on the left side of the road. The traffic and in-car shots are all US/European.
Continuity mistake: When Jack and MacGyver jump out of the window, after they land the fire extinguisher by MacGyver keeps changing position from in his arm to on the ground.
Factual error: All the information regarding Germany and there train system are wrong. All the fast trains (InterCity Express) in Germany are electrified and therefore no-one could land on the top of the train with a helicopter. Also the trains have a completely different design and the train station in Berlin and Frankfurt have a completely different look.
Continuity mistake: When they get to the warehouse the door to the van closes, the shot changes it closes again.