Damage's head falls off when he is thrown off the roof by Frank, but in the cutscene following it, Damage's head is still on his body.
At the beginning of the Ryker's Island level, Frank will start outside of the interrogation room, but the door is missing and if you go through it, the locking sounds are heard and Soap and Molly will be gone.
In the opening of "Grand Nixon Island" level, Punisher is seen wearing war-paint resembling his skull logo on his face. But when the level starts, the paint is gone having his face cleaned like every other level of the game.
An M60 doesn't have 4 round burst. It is simply full-auto.
Almost all firearms experience muzzle climb as the result of recoil, yet the weapons used by the Punisher in the game show no such effect. This is more obvious when firing full auto since an entire magazine may be fired in one go without any real effect on the predetermined accuracy of the firearm.
A desert eagle hold either 7 (50. cal AE) or 8 rounds (44. mag). Not 6.
The magnum revolver (either S&W 500 or 460) holds five rounds not six.
If someone really was to have their head submerged in a tank full of Piranhas, as seen in the 'Zoo' level, it is highly implausible that their flesh would be eaten at all, let alone within a matter of seconds and with enough ferocity to cause near instant death. Although omnivorous, the aggressive tendencies of Piranhas are heavily exaggerated, something which is common in video games and films alike.
Some of the newspaper images contain text taken from the design documents for the game.
In the Ryker's Island, Frank can perform quick kills with his knife even before adquire weapons. If his weapons were requisitioned when he was arrested, his knife should too.
In the newspaper clippings about Ma Gnucci's death, Ma Gnucci appears without her arms and legs (since this image is taken from the "Welcome Back, Frank" comics where Frank teased a polar bear to attack her at the zoo). Here, Frank just invaded her office and threw her out the window.