Plot hole: Where did Cross get the blood on his hands? The gloves were clean of blood after he looked at the teeth and removed the gloves, so where did it come from?
Plot hole: Not far into the movie, Starla decides to check out the basement to see what Grant's been up to. As soon as the door is opened she reels from the stench and we discover that it's full of rotting meat and dead animals. In reality, the whole house would have smelt like an abattoir for days before hand and the stench would have permeated out into the neighbourhood. A non-airtight wooden door would not have kept that kind of smell located to the basement only.
Plot hole: When Magneto lands the bridge between San Francisco and Alcatraz, only the ends of the bridge are on land, with the rest still suspended in the air despite having nothing to keep it there. Magneto could arguably be using his powers to keep it supported, but at the moment he loses his powers it still does not collapse at the center.
Plot hole: If the gasoline in fuel lines and tanks is reaching flash point and exploding, there should not be so many cars just sitting around. Surely all of those vehicles' tanks are not dry.
Plot hole: When we see the Zenith Team playing softball, it's a scene taken from later in the movie. For one thing, Mr. Pibb is there, even though we don't meet him until the next scene. Second, they're in the room with the UFO, but we don't see that until later. Finally, Zoom's outfit is different than the last scene, but in the next scene he's wearing the same outfit.
Plot hole: Just before the bomb explodes at the beginning of the movie, the guard is looking for the car playing 'don't worry baby' on it's stereo. In the final timeline the disaster has been averted, the bomb having gone off, and the ferry docked. After this, when Carlin is in the car, the same song is playing, but the bomb was set to a timer.
Suggested correction: That's why the movie is called Deja Vu and thats why Carlin gives the girl such a strange look. The song triggers a feeling of Deja Vu for him and it almost feels to him that he knows her. Besides, a different station could have been playing the song.
Suggested correction: The first time it plays comes off the radio. The second time we hear it mid-play. It could have come from a different station, the same station could have played it again later, or a CD or cassette being played in the car.