What if MR was angry not at Dylan but because of Dylan? We know Dylan had been moved six hours away from his father, we know that custody was changed to MR's disadvantage, we know that child support was changed to MR's disadvantage, <modsnip>, we know that Dylan spoke to the family court Judge in private, with sealed records. All of that paints a picture to me of an MR whose world is crumbling, and there before him is the one person who represents all of that - Dylan himself. Not Dylan's mom, not the attorneys, not the judge, not Cory, not MH, but Dylan.
And then Dylan is a day late getting there, cutting into MR's time with his son. Dylan's tired, he's probably cranky and hungry, he's distracted texting all his friends, he's frustrated with the poor cell reception, his dad won't let him visit his friends that night..........
Add that in to MR's obvious (to me) lack of emotional maturity and I can see a lot of reasons why anger might have been a factor in whatever happened to Dylan. And that could have been expressed in either some premeditated act of abduction/hiding, or impulsive physical violence/harm to Dylan.