Other mistake: Snake is taken to the sports arena. We see a man in a basketball court racing a timer to score hoops. He fails miserably and is riddled by dozens of gunmen stationed all around the court. The crossfire would have killed more than just the unlucky basketballer.
Other mistake: When the President asks someone to connect him to the White House to talk to his warn his wife as Cuerva threatens the power outage, an extra hands him the phone, but does nothing to contact the White House (OK, someone off-screen could be doing it, but the President was talking directly to this extra). A mere 3 seconds later, he is asking the (White House) operator to connect to his wife. Just 1 second after that, she's on the line.
Other mistake: When Snake lands in LA in the sub, it shoots out of the water, lands on a concrete pier, and hits a wall at a very high speed. Its future technology must be why it doesn't crumple up like a tin can; but Snake exits the sub just fine, despite there being no apparent safety harness. As this is just a decade or so in the future (and not a century or more), it is highly unlikely that this society's technology has advanced to a state where the basic laws of physics can be broken.