During the bomb disposal mission, Pliskin mentions "the heliport on Strut H". Strut H is clearly visible from several of the connecting bridges, for example, the bridge connecting Shell 1 & Shell 2, and there is no heliport on top of it. The strut next to it (Strut I) does have a heliport, however. This was due to a modeling error.
During the Strut B encounter with Vamp, Pliskin's wrist is badly cut. This cut is missing completely moments later when he meets up with Raiden and Stillman in Strut C.
In both the end credits and the citation of the quote at the beginning of the Plant Chapter, the name of the Smithsonian Institute is misspelled as "Smithonian".
Raiden is able to talk on the codec even in underwater.
On top of Federal Hall, Solidus tells Raiden that George Washington became the first US president "200 years ago today". Washington was inaugurated on April 30, 1789, but this scene takes place on the same day in 2009 - 220 years later, not 200. This is because Solidus is intentionally rounding the number down, presumably to make his "speech" flow better.
Every single hostage in the Shell 1 B1 Core has hands with a "white" skin color, even though many of the hostages are black.
Unless Scott Dolph is short sighted he would have seen Snake taking Pictures.
As Snake opens fire on Fortune inside Arsenal Gear he lets out a battle cry that sounds like "Hrraaaaaah!" Yet the subtitles read a grunting sound "UNHh!!"
Whenever Pliskin, Raiden and Rose mention the former leader of Dead Cell, they refer to him as "Colonel Jackson". Since Dead Cell is said to be a U.S. Navy unit, and the rank of "colonel" is never used in the Navy, he should be called "Commander Jackson". (Dead Cell member Vamp later refers to Jackson with this correct rank, so these errors were most likely intentional.)
Raiden questions why the nuclear football, which the president of the United States can use to authorize a nuclear strike, was brought along with the president to the Big Shell facility, and the cyborg ninja explains why. Both ought to have known that the football goes everywhere the president goes where there isn't a fixed command center, in case a situation arises in which a nuclear strike must be launched on a minute's notice.