Other mistake: When Agent Wells tells the White House they need to alert the Pentagon that Lozano is inside the Pentagon, she is told "it's already done, they are locking down the building right now." Then, later in the same episode, we see Lozano use a key card to easily pass through the building. (00:15:45 - 00:21:15)
Misalliance - S1-E19
Other mistake: When Patrick Lloyd receives the text message on his phone while working out, we hear it buzz and he reads it immediately but the message says "14 min. ago." The time also jumps from 12:15 to 12:59. (00:02:20)
Answer: It's a recurring theme on the show. Characters come and go depending on the storyline. General Cochrane, Tyler Richmond, Abe Leonard, etc.