When Finch finds Root in her cage with Bear, he puts his right hand in his pockets. When Bear sits beside Finch, his hand is out of the pocket and hanging by his side, then the next shot Finch's hand is back in his pocket.
When Bear leaves Root for Finch, he sits beside him, but in the next shot he's behind Finch, looking to Finch's right.
When Reese enters the motel he's heavily wounded but during the battle with US marshals in the hallway he doesn't act or look injured at all.
More than 10 Russian gangsters arrive in front of the hotel where Root shots 7-8 bullets at them without even looking at their direction and it is said that they are all dead as a result of this which would have been impossible.
When Reese is shown in the flashback, the Machine view shows him with yellow color, signifying that he knows about the machine, even though he had not yet even met Finch. In previous flashbacks to times before he met Finch, he had various colors depending on his status at that time, but never yellow.