Using the noclip cheat, Hudson is seen holding an AK-47 before entering the interrogation room, but when Hudson opens the door, the AK-47 disappears.
Mason can be heard saying "Oswald...compromised!". as well as "Kennedy...John...Fitzgerald". This is refering to Lee Harvey Oswald who was the alleged assassin of John F. Kennedy, and implies that Mason killed the President and framed Oswald for the crime. This is reinforced by the game's final cutscene in which archive footage of President Kennedy prior to his assassination is shown, revealing Mason in the crowd.
Three days prior to this level, Weaver sent an email to Hudson, proclaiming that he had lost faith in Mason, who he felt could not be trusted. He believed that what happened in Baikonur, Kazakhstan, was "more Woods' doing". He felt that the Russians had got to him, and they should just kill him once they had extracted all information from him. This explains his plan to get to the bunker and leave Mason to die from Nova 6.
There is a subtitles mistake in where the rocket takes off, when it says that Mason says the line "Okay, time we got the hell out of here.", even though this was actually said by Woods. The next line is similar, it will say that Woods says "Not yet, we need to find Dragovich.", even though this line was said by Mason.
In the room after the flashback, if the player passes or stays by the body in the body bag, they can hear it laughing.
After Mason punches Hudson, if the player goes to the right of the torture chair the player can see a small TV that still is recording the torture chair, but it shows Mason in it closing his eyes.
The console computer that the player can access in the main menu is not there when the player gets out of the chair.
On the Wii version, all sections where the player can control where Mason walks are gone, and the entire sequence is simply a pre-rendered video of the level from the Xbox/PS3/PC versions (as evident by the higher resolution models and lighting effects). Also, there are many more video and audio distortion effects, presumably to skip over sections where the player was supposed to control Mason. Some lines get cut as well, such as Hudson arguing to Weaver that Mason knows where the broadcast station is.
There is still intel on the Wii version. All three intel pieces are automatically given to the player after the cutscene.
During the Vorkuta sequences with Dragovich, Kravchenko, and Steiner, while not restrained as Mason, it is possible to move around as if the player were a character. However if the player bumps into anyone, they will not register the player.
When Hudson says that Reznov is dead, the flashback of the level "The Defector", Reznov is seen holding an AK-47, but in the actual level, he holds a Commando. Reznov is also seen using an AK-47 during Victor Charlie segments on one of the projectors, though he uses a Commando in that level as well.
When the player leaves the room where Hudson gets knocked out, they can see two closed doors; one in front of them, and one to the right. If the player walks very close to the right one, a beast can be heard growling.
The flash-back to Vorkuta seems to take place inside a smokestack, which may be a reference to the movie "Brazil". Additionally, parts of the interrogation room are similar to the one seen in "Brazil", especially the chair and the table full of torture equipment
After entering into the lab where Mason remembers what happened in Vorkuta, you can see Dragovich, Kravchenko, and Steiner. Kravchenko will be wearing the same outfit that Mason/Reznov was wearing on Rebirth Island.