Revealing mistake: When the leading hitman jumps from the balcony you see him land on a rubber mat.
Character mistake: A TV news announcer describes Alan Shepard's first manned launch into space as him being lifted to "an altitude of 116 miles per hour." That's not an altitude, that's a speed. It should have just been "116 miles."
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.
Factual error: During the 31st year of the Avalon's voyage, the ship passes close to the star Arcturus, which is about 37 light years from Earth. Later in the movie, it was stated that the Avalon was moving at around 50% of the speed of light. The ship would not have reached Arcturus in the time allotted.
Continuity mistake: When the Senator is about to be sacrificed, the cloth on her mouth immediately disappears for a split second. (01:29:35)
Factual error: In the first scene where Dr Strange is preparing for surgery he uses improper surgical gowning technique breaking aseptic protocols. Strange puts on a mask after washing his hands, contaminating his clean hands by bringing them in proximity to the non-sterile environment of his face. Surgical masks must be worn before the full washing of hands. Another error is that he inserted his hands all the way through his gown to don gloves. Hands must never leave the sleeves and gloves must be put on with the sleeves still covering.
Plot hole: Searching for the source of the river, the raft is going downstream. Return trip it's also downstream. Generally, no matter where they are going, the rafts keep floating downstream.
Factual error: In the movie, we see the Statue of Liberty with its current bluish-green color. The statue only got that color over time, and as it was still being built, it should be its original brown.
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.
Factual error: When it's 00:00 on January 1st, it's not night in Sydney, it's 11 AM. When they 'reveal' stuff at the end of the movie, and they show that things happen exactly at 00:00 in the night in London, it can't possibly be dark in Sydney, Australia.
Factual error: Scenes of the CGI Airbus A320 do not show the RAT (Ram Air Turbine) deployed. When the A320 loses power in both engines, the RAT automatically deploys to provide minimal electrical power to the plane. (01:20:05)
Visible crew/equipment: When Dewey is introduced and has a phone call with Jeffers about the leak, he is packing away files in a briefcase. On his desk there is a pad of paper beneath Dewey's mobile, and the scripted lines for Dewey's side of the phone conversation are handwritten on the top sheet, not being removed from set prior to filming. (00:08:25)
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.