When Johnny is taken to prison, he's still wearing his civilian clothes. Not only is this non-standard procedure in American prisons, but the two prisoners being transferred with Johnny are wearing prison grays.
In real life, in the prison system in USA, prisoners who are awaiting trial, like Johnny, are never housed in the same prison with already-convicted prisoners, especially, not with prisoners serving very long sentences.
Any number of tests would show that there was no gunpowder residue on Johnny's hand, and he didn't shoot Vince.
Somehow despite the fact that his cell is locked, Dayton gets inside of it through the metal bars, even though he is supposedly only invisible.
The first time Johnny sees Dayton in his cell, Dayton turns visible when he removes the jacket. The second time, Dayton turns visible without removing the jacket.
It's never said how Johnny was released from prison, apparently for killing his own father. Jack even says earlier that even if they take care of Dayton, it won't clear Johnny. And there's no reason why it would.