Factual error: During the scene in which the plane flies directly toward the ground at a speed of 2070 knots to deliver the bomb, after dropping the bomb and pulling up to fly horizontally through the city streets, there is no damage or anything created from a sonic boom. At that level and speed, the sonic boom would have been tremendous on the ground, even if the plane was designed to minimize the shock wave.
Continuity mistake: In the beginning they are on the U.S.S. Abraham Lincoln (CVN-72). Later they are aboard the the U.S.S. Carl Vinson (CVN-70) and end up on the U.S.S. Nimitz (CVN-68), yet the personnel are the same aboard all three ships.
Factual error: The Talons and EDI take off on their first mission from the Philippine Sea, which means they have to fly west to reach Myanmar. They're travelling at Mach 4, and it's still daytime when they set off. If you travel west at supersonic speeds, you're actually outpacing the sun, effectively turning back the clock. But when they get to their target, it's dark.
Continuity mistake: At the end when the two pilots are talking, Jessica Beil's character has steri-strips on the cut on her cheek, but the arm she got shot in isn't even in a sling and she seems to be using it just fine. The cut on her cheek would have healed long before her arm would have. She was also limping quite badly when Ben rescued her, but she stands/walks just fine here as well.
Plot hole: After E.D.I. goes rouge, Kara brings up his weapons list, which consists of 2 ThroatRippers, 2 ShockHammers, and 3 Blue Ferrets, so E.D.I. has 7 missiles. He fires two during the Russian dogfight, another two when he and Ben escape from Alaska, and another two at the Korean border - one of which is the last missile. That's 6. So where did the last missile go?