Factual error: When the fighter jets get ready to shoot down the jumbo jet from behind, Baker sends an SOS 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 SOS, let alone be decoded so quickly and repeated in such a short time?
Plot hole: After Jaffa is captured the news gives a full report of Jaffa being held captive on an American warship in the Mediterranean. Why would the media know who was captured, who captured him, and where he was being held? This was a covert operation to capture the worlds most wanted man, the media shouldn't know any of this.
Plot hole: Not counting Altar or the Sleeper we know there at least 8 other terrorists on the plane. One of them is killed by Altar himself and five of them are killed by the strike team. What happened to the other 2 terrorists?