The Boeing 737 the inmates board has a conventional straight wingtip. The 737 that is shown touching down is obviously not the same aircraft because it has a set of tall winglets on the wingtips.
The Justice Prisoner and Alien Transportation System operates MD-83s and Boeing 727s, not 737s.
When the men enter the plane, clapping can be heard despite all the prisoners hands being handcuffed. It is actually possible to clap while handcuffed.
Muskegon is on the west coast of Michigan on the shore line near the middle, not at the bottom of the state as depicted by Mazall.
It makes no sense for either Piper or her lawyer not to ask for witness protection and some sort of deal in exchange for her testimony about a major drug trafficker. It also makes no sense for the prosecution not even to approach her about these issues long before she takes the stand, especially given that she is a well-educated white woman. State prosecutors in court will only ask questions from witnesses under oath that they already know the answer to, and that they ideally can prove by other evidence, so they can then pressure the witness even harder if caught lying under oath, and extract even more information.
It makes no sense for Piper not to bring up the incident with Doggett and Healy with her lawyer where she almost got murdered by the deranged inmate while the correctional officer looked the other way.