After Aki removes the phantom particles from Gray, she picks up a canister that's hovering in the air, when she originally placed it on the table further away.
Deep in the Gaia crater, Gray tries to fend off Phantoms, and shoots a group of them to his right. After a brief cut where he stops shooting, he's pointing the gun to his left.
In the beginning of the movie when the protagonist is logging her dream the date info for the it is 12.13.01 when in fact it's supposed to be 12.13.65.