When McGyver offers to fix the speaker phasing on the wardens stereo in his office, he takes the cover of the receiver off and starts turning the trimmer capacitors for the radio tuner section, and this would do nothing more than louse up the tuner alignment. Actually you would just reverse the connections on one speaker lead to accomplish this.
The simulated helicopter sound using the ceiling fan has some flaws. The buzz of the tail rotor (which tends to be the loudest sound made by a helicopter), the turbine whine and the rush of the jet exhaust from the Bell UH-1 Iriqiouis are not duplicated, although these sounds are dubbed in by the sound department.
MacGyver uses a trail of gunpowder to blow up the truck which would have not worked as shown. For gunpowder to explode, it must be confined in a tight package when it's detonated. As seen here, it would have just burned out and not exploded.