(at around 1h 10 mins) After the lights go off, some goons shoot at where two characters are standing, only to find them gone when the emergency lights come on. Not a single bullet hole is visible in the Japanese paper screen they were standing before, however.
(at around 1h 11 mins) While Frank Castle is fighting a Japanese Swordsman, a holstered gun on Castle's back disappears. Moments later, it re-appears in the holster. The weapon wasn't touched by anybody.
(at around 1h 15 mins) When Frank fights Tanaka's daughter, after he pins her to the wall, she takes both her earrings off and scratches him. In the next shot her earrings are back on and then they're gone again.
When the Punisher is arrested, a newsreader says that he has been charged with 125 murders, even though that was the amount of murders he had committed before the movie takes place, and he had killed a lot more people since then.
The police haven't been able to identify The Punisher even though he handles his weapons without gloves and leaves them behind at the scene of every kill.
Frank in a fight with the Russians gets knifed in the shoulder. and blood soaks his shirt. Later when Joan cuts his shirt off to attend to the wound there's no blood on his chest or around the wound.
In a long shot of rack-torture scene, everyone is clearly standing on a place-marker.
The "Peter Bear" scene when the Yakuza kidnaps the two girls. Both suppressed shots go through the panda, not the woman, yet she slumps backward dead.
(at around 1h 10 mins) After the Japanese henchmen are shot at through the paper screen, the very last extra to be shot dies unconvincingly. He slowly drops to his knees, leans forward, and carefully places his weapon down.
When Frank Castle escapes from the rack (stretching table), he is slowly unscrewing the wingnut on the metal clamp holding his hand in place and as he is still doing so, he calls the two men over. Just as they arrive, he unlatches the one wrist clamp but somehow, suddenly, both hands are free enabling him to shoot them down. He could not have had time to undo his other hand during that sequence.
(at around 47 mins) When detectives Berkowitz and Leary go down into the sewers to search for The Punisher's lair, Berkowitz explains how he met Frank Castle. As they round a corner a film crew member's leg is visible in the corner of the shot, and they quickly move their leg out of the frame.