Revealing mistake: Costigan carries a Walther PPK/S. The hammer on his pistol is down both before and after he shoots the junkie armored car thief. The shot to the leg should have automatically recocked the hammer.
Continuity mistake: When Jack Nicholson approaches a young Matt Damon he has a cigarette dangling from his mouth. When the camera faces Nicholson he has no cigarette. (00:04:55)
Continuity mistake: When a shootout between Sullivan's men and Costello's starts after Queenan's death, one shot initially hits the left glass of the van, then in the next shot the glass is intact, only to be hit again.
Character mistake: During the funeral at the end before the 21 gun salute, the NCOIC called for "half left face", that would cause everyone to get shot in the face.
Suggested correction: Half-left face means a 45° left turn (left face is a 90° turn), so wouldn't result in anyone getting shot.