Ole' Miss outplayed Penn State, and had the better game plan.
The final score really wasn't as close as its 13 point margin would indicate, since Ole' Miss was leading by 21 with just a few minutes left to go, and was playing mostly prevent at the end to eat up clock time.
If this were a one score game, maybe Franklin's complaints might have had some more noteworthiness to them, but given how Ole' Miss basically controlled this game, he would have been better off simply wishing the Rebels well, and moving on.
Just about every game has more than just a few bad calls. It's part of the game, and you have to get your team good enough to the point where those calls don't affect the outcome.
Heck, we could complain about some of the officiating in the 2020's season Rose Bowl, but the fact remains that Alabama outplayed us and outgunned us in that game, to the point where those calls really didn't matter.