Thrill Kill - S5-E1
Factual error: When Dylan gets out of jail, a palm tree can be seen in the background behind him. This reveals that the scene was filmed in Los Angeles, not Philadelphia.
In the Dark - S4-E22
Revealing mistake: When Tony is telling Gibbs & Ducky that Abby got a hit on the dead sailor's fingerprints, Gibbs takes the file from Tony; the camera shows the file, which appears to be a legitimate profile sheet, but in the comments section, is the script that Tony just read aloud. (00:07:36)