In all intro cutscenes for the flashback missions, both Danny and Leo are in the cutscene, but only Leo is involved in the actual flashback levels.
In the intro cutscene for Assassination, the Project Militia are holding Spas-12's. The shotgun is not in the level at all and Spas-12's are not anywhere else in the game.
When Danny climbs over the dumpster in Most Wanted to get over the fence, he is not shown carrying any weapons on his holster or in his hands.
Sometimes a glitch can occur in Assassination, where after the lift is called to the first group of Project Militia, the light does not turn on and the Project Militia will just stand in the hallway. If they see Leo, they will ignore him.
The AI can repeatedly run forward and backward until they spot the player or the player attacks them.
In the PC version, Leo can run up in front of the gas man in Ritual Cleansing and he will not chase Leo until he spots him again.
In all versions except the Wii and PS2 beta, Dr. Whyte's mouth movements when she says "Pickman thought his mercenaries could destroy Leo. I believe the only person who can stop him, is you" do not match in the intro cutscene for Domestic Disturbance.
In the PC and Wii versions, the shotgun reload audio does not match the animation.
In the ending for "Release Therapy", Danny/Leo wakes up from his comatose state and washes his face with his glasses still on.
In the opening cutscene for "Broadcast Interrupted", Danny rubs his eye with his glasses still on. In the beta version of the game, Danny takes off his glasses first.