The GX-1 is a 2 seat F-14, the plane they show getting shot down is a one seat F-5 . The footage of both planes is actual footage from Top Gun.
The pilot of the GX-1 never fires a weapon before he ejects. However, right after he ejects, a Russian Mig is seen going down in flames.
In the last scene flying over the mountain (before commercial break), the burner flame can be seen even though there's no fuel and the propane tanks had been dropped to the ground.
The beginning stock photography of the Alps shows snow covered mountains which doesn't match MacGyver's location shot in Canada in late summer.
During the "Top Gun" dogfight sequence, the editors strung together shots from several different points in Top Gun. At one point, the planes are clearly flying over the desert, another, they're over the ocean. When the GX-1 hits the afterburners, it's clearly a take-off shot (gear is down).
Pete tells Mac they've lost the plane "somewhere in the Alps" and that it's crossed over the border into East Germany. The closest the foothills of the Alps get to the former East Germany is 190 miles to the south in central Austria. Given that Mac is with a "Swiss Miss", we might infer he's in the Swiss Alps, which would make the East German border 230 miles away.
The hot air balloon MacGyver was flying in had a Canadian registration and not Swiss as it should have being in the Alps.
Nikki offers to buy the animal from the farmer with a handful of Deutschmarks. To an East German, the currency of West Germany would not only be useless to him but illegal to possess. Her money would have been worthless to him.