Jerry is shown as Tony's magical assistant, helping him set up illusions. However, in the first half of the season there was no indication that Jerry was anything other than Tony's pilot, and several indications that Tony had other assistants like Connie and Larry.
Tony is apparently shot in the leg, since he hobbles away from jail. However, later although he limps slightly, all we see is a bleeding graze on his forehead.
Johnson holds up a handkerchief as protection from the fumes generated by the man burning through the vault lock. However, the man doing the burning has no such protection and suffers no ill effects.
At the end, Janet worries that Charles will never forgive her. For what? She was only captured by Gunther and used as a hostage because of Charlie's criminal past. If anything, he should be seeking her forgiveness.
In the abandoned jail, Lomas immediately identifies Tony, even though he never got a look at him except the back of his head in a dark corridor.