Continuity mistake: It was briefly stated in the second film that the T-Virus was created by Dr. Ashford to cure his daughter Angela and that the Red and White Queens were based on her. This movie contradicts that by suggesting that Dr. Marcus created the T-Virus to cure his daughter Alicia, and that the Red/White Queens were modeled after her. While the rest of the movie stays true to the continuity of the previous films, this rather obvious ret-con is still a major continuity gaff.
Continuity mistake: He cuts a hole in her pants for insemination. When in the car moments before fighting the dog there is no hole.
Continuity mistake: When the Senator is about to be sacrificed, the cloth on her mouth immediately disappears for a split second. (01:29:35)
Continuity mistake: When the police are moving in to arrest Dzhokhar Tsarnaev, the shot shows an FBI SWAT officer grabbing him. But in the next cut, the officer changes to a Boston Police Officer while changing back to a FBI Officer in the following shot.
Continuity mistake: When Mrs. Otterton is in Chief Bogo's office holding her family photo with both paws, in the wideshots her purse is hanging in the crook of her left arm, but after a brief shot of Judy, when it cuts to Mrs. Otterton's closeup as she tells Bogo about her two beautiful children her purse is gone, then after another brief shot of Judy the purse is back in its place again in the wideshot.
Continuity mistake: When a bunch of guys are out back passing around a bottle of liquor, the amount of alcohol in the bottle increases at one point.
Continuity mistake: After Dory reads the wall map while she's in the glass carafe, when Hank hides behind the rolling cabinet there's a long shot of the corridor with him at the far wall, then in the next shot from behind Hank a drinking fountain has suddenly appeared on the wall to the left, between two pictures.
Continuity mistake: Strange is at home, looking for help on a video chat. His friend says no, and in his rage he sweeps almost everything off the table including the Microsoft Surface laptop. Christine enters with food, we cut back, and the area of the table to his left, which was totally clear a second ago, now has several pieces of paper on it and the laptop with a closed lid. A few moments and cuts later, the laptop is in perfect condition on the table with lid open.
Continuity mistake: The doctor starts out carrying a Holland and Holland "Royal" Double Rifle; but when he and Tarzan pursue the train, the doctor loses his H&H rifle in the leap from a cliff. Lo and behold, after they commandeer the train and disembark, the doctor is inexplicably carrying his H&H Double Rifle again. The H&H is not a common rifle, even today, and his chances of just discovering an exact replacement aboard the train is beyond coincidental.