Are the targets you have posted still at 5 yards? If so, there is practically no way that something wrong with the gun could cause it to shoot that far off at that distance; you are definitely pulling your shots low.
.45 M&Ps generally have exceptional accuracy, the .40s are generally average, and the 9mms commonly (though not always) have accuracy problems. That said, it is unlikely you would notice any difference at distances of 15 yards or less.
All targets were posted at 5 yards