During the fight scenes between Spencer and Mikel Dayan, the scar on her chest (which she shows Spencer later in the bar) is absent.
Instant pudding powder isn't truly instant; it must be stirred and chilled in the fridge in order to set. Just pouring the powder into the water would not be likely to slow the motion of the bomb.
During the "geek battle" between Hardison (Aldis Hodge) and Chaos (Wil Wheaton), Chaos' computer doesn't have the battery plugged in or any visible power source. That HP model has a battery that exceeds the size of the base of the computer.