Factual error: The crew sent to board the ill fated jumbo jet is in the "Remora", which is clearly a modified F-117A Stealth Fighter, but retaining the same dimensions. It would be physcially impossible to fit that many people and such a spacious cargo hold into a plane that size with the engines. In fact, with the additional weight, the engines would have to be even bigger for it to operate.
Factual error: When the fighter jets get ready to shoot down the jumbo jet from behind, Baker sends a Morse code message via the plane's rear lights to the fighter pilots. From such a short time of the fighter pilots viewing the message, they were able to immediately decode it as "Hail Mary, Alpha 1, 10 minutes. "Message repeats" says fighter jet pilot. Wouldn't it be impossible to send such an elaborate message via Morse, let alone be decoded so quickly and repeated in such a short time?
Other mistake: How come when they are on the Remora F-117x the pilot is the only one wearing an oxygen mask? The team only has headsets on but they're all in the same space - just before they dock, Kurt and Steven stand up and move forward straight into the cockpit area next to the pilot.
Plot hole: When the fighter jet broke off from the 747, Steven Seagal died but the pilot ejected and was not killed. The people in Washington don't know that the team made it on board the 747 until later when they got signalled with the plane's tail lights, but the fighter pilot that ejected would have told Washington that the team made it on board.