Factual error: As the two fast boats start heading up river towards the finale shootout, one boat has its navigation lights reversed. It has a red light on the starboard/right side, and a green light on the port/left side. It should be the other way around. (The lights on the other boat are correct.)
Continuity mistake: When Naomie Harris wakes up in the trailer after being abducted, she is rigged with a bomb around her neck. During the scene there is sunlight coming through the window of the trailer. The problem is that the whole section of the movie beginning, when she's abducted till she's in the hospital, takes place roughly between the hours of 2:00 and 4:00 A.M.
Continuity mistake: In the series of shots when Crockett and Tubbs have phoned headquarters there are several large red LED clocks in the background. The clocks jump ahead a few minutes with a few seconds on the phone but the funniest clock change is at the end when the minutes showing actually go backwards from 49 to 48.
Other mistake: When Ricardo is translating the email while on the ship, he chooses the origin language as English and the destination language as Spanish. But when he presses translate, it translates from Spanish to English. (01:20:20)