Continuity mistake: When Chandler is on the vidcom with the president, the digital clocks on the wall behind her only tick to 20 seconds into the 10th minute of the hour, then reset back to zero seconds.
Continuity mistake: While trying to restart the engines after the ship is hit by the nuke's EMP, Chandler is checking the fuses while Chung is going through his checklist. There are only five visible fuses in the six available slots in the panel that Chandler is checking. After he gives the order for Chung to "give it a kick-start," the slot which previously had no fuse now does, only for it to shoot out from the start attempt.
Continuity mistake: Captain Chandler states that the ship is going to an "unmanned fueling and food station outside of Guantanamo." When they get there, it's the main base, not an unmanned station.
Continuity mistake: When the doors are chained closed and are fired upon by the enemy, the bullet hole locations on the doors are different on the interior and exterior. (00:25:00)
Continuity mistake: The "real" time between the end of season 1 and the beginning of season 2 is supposed to be 1 day, but Tex's hair and beard are 2 inches longer.
Unreal City - S2-E1
Continuity mistake: While Lieutenant Granderson is being escorted around the compound and walks to the class, she is wearing O-3 rank (two silver bars) on her collar, despite never being promoted during the show to this point. Later on in the episode, when she is talking to her mother, she is wearing O-2 rank (one silver bar) again. (00:13:35 - 00:34:15)
Continuity mistake: Chandler is reviewing the President's paperwork and finds the manifests which brought his wife and daughters from Washington (document dated 07-05-13) and his son from Detroit (document dated 08-02-13). He then checks the computer for casualty figures in Michigan where the son was originally from (dated 8/4/14-onwards). So the plague hit in early August 2014, but the documents show the family leaving their home a full year earlier. This is not a plot issue (no, they did not fly out a year prior to the plague), but rather a prop-maker error. (00:28:00)
Continuity mistake: In the previous episode, Doc Rios says he can hardly see anything without his glasses. In this episode, still without his glasses, he looks out of the hut window and describes the compound beyond in detail.
Continuity mistake: They are in a minefield. The map shows it's between a bunch of islands or small landmasses. All the dialogues and maps reflect this, but the visuals show open sea.
Continuity mistake: After season 1, then Captain Chandler is shows with a Silver Star Medal. But in season 5 he does not have it any more. Considering his status in overall and the fact that he has not lost medals/awards that are considered higher, his Silver Star would not be revoked from him.