At 36:53 Reese's hood clearly falls down while fighting. In the next scene it is back on and remains up for the rest of the fight.
Right at the end of the anonymous chat, Root clearly types an 'S'. Harold appears on the screen but obviously doesn't contain a 'S'.
When the assassin turns to enter the subway bathroom a man in a green hat is entering immediately before him. When the camera changes to the Machine's POV, the man is gone.
When Finch is tracing the Trojan horse of the tracker we see "Accessing network on IP 623.173.93.225.9". IP addresses contain 4 number groups, separated by dot ("."). Each number is between 0 and 255. So a valid IP would be for example 62.173.93.225.