Two reasons were given.
One is that the film apparently implies that the Jews built the Pyramids, a very touchy subject in Egypt.
The second is that the film characterizes the splitting of the "Red Sea" as the result of an earthquake, not as a direct miracle from Allah.
The Koran does discuss the Exodus story, including the splitting of the sea, in chapter 26.
Morocco censors also banned the film, but they did it after some theaters started the first showing, causing much confusion. No official reason was given, but Morocco had also banned the biblical film Noah.