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?