Continuity mistake: When Snake falls toward the water with the "kingpin's suitcase", the gun is in his right hand and he's gripping the heavy suitcase in his left hand. Yet, in the last shot of him underwater the gun and suitcase have switched hands. Interestingly this is not a flipped shot, the watches are still on his left wrist.
Continuity mistake: When Stanley Tucci throws his wallet at Tom Sizemore in the bar's robbery scene, the wallet hits Sizemore in the face, then hits his upper arm, then falls behind him to his right. Yet, in the next shot, it has landed on the bomb case on the floor to his left. The same thing happens a few moments later when Tucci throws his keys at Sizemore.
Continuity mistake: On the airplane, when Eliot pushes the suitcase down the stairs, Snake grabs hold of it with his left hand and while holding the gun in his right hand with his right wrist around the stair bar. In one shot the gun is gone and he's gripping the stair bar with his right hand, then the gun reappears again.
Continuity mistake: When Desalvo's bullet hits Arthur Herk's TV the glass shatters and the bullet hole is visible on a black background towards the upper left. But in following shots much more of the glass is intact, with a large jagged hole in the glass surrounding the area of the bullet's impact.