Continuity: When John Travolta is searching the dead woman's house he has latex gloves on. When he pulls out his gun and heads into the basement, his gloves are gone when he turns on the light. Then they reappear a few seconds later.
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Mistakes
When Travolta is driving his car backward from the crime scene with Madeleine, the scene shows the soldiers moving away trying to avoid the car, then the scene changes and changes again showing the same soldier's movement. See more...
The General's Daughter mistakes
Factual error: Throughout the movie the "HMMWV" being used in scenes are civilian Hummers painted green. They are easy to spot since they have 3 orange lights on the center of the windshield, where as military HMMWVs do not.
Factual error: In the beginning where John Travolta is going through the gates in his car, he stops to let the guard on duty see his military ID. Under the US seal it has the words "1ST Sarg." printed. Real military ID's would have "1SG / E8" printed on them where he has "1ST Sarg." printed. Also, his expiration date says "12/24/02". This would be printed as "2002DEC24".