- Incorrectly regarded as goofs: The movie is plainly set in an "alternative" reality, so apparent errors of history and geography can be discounted. We don't know how many World Wars there have been in their reality, nor when films, etc, were released.
- Continuity: The first newspaper shown reports the Hindenburg III docking at the Empire State Building on October 6th, 1939. But in shots of the newspapers shown during the montage after the first attack by the robots, you can clearly see the date of publication was March 15th, 1939. And later, Polly says that the current date is March 2nd.
- Continuity: When Sky Captain and Polly are running across the log bridge, he fires a 1911-style semiautomatic pistol at one of the birds. When he falls and drops the gun, it's the revolver he used against the robots earlier in the film.
- Factual errors: Polly never cocks the shutter on her camera and never seems to advance the film. In one close-up you can see her middle finger resting on the cocking lever in its uncocked position.
- Revealing mistakes: When Polly Perkins first exits the theater after meeting with the scientist, there are duplicates of the people in the crowd around her.
- Continuity: The bones of the doctor who was burned to the bones before Totenkopf's message are gone when the camera zooms in at the steel walkway.
- Continuity: In the sequence where the winged robots attack on the military base, Sky Captain chases the lead robot. During his pursuit, he flies his P-40 airplane over an exploding Zeppelin. He is clearly flying above the fiery Zeppelin in one shot, but in the next shot, the P-40 appears to be below the zeppelin.
- Factual errors: In the first thirty minutes, Polly Perkins is admonished about taking pictures. She has the trusty Forties Argus C-3 which had to be hand cocked every time. She is seen taking a photo, the sound man has added the proper shutter sound, but the cocking lever does not move and was seemingly never cocked as it remains in the "released" position.
- Continuity: When Polly reaches for her camera on the tree log, Joe grabs her right hand and the camera is in her left. In the next shot, he's holding her left hand and the camera is in her right hand.
- Factual errors: The rocket's display showing its height contains two spelling mistakes (assuming it's written in German as the other labels in the rocket): "VERSTARKER" (booster, amplifier) should be written with A-umlaut and the plural of kilometer is simply kilometer, without s at the end.
- Factual errors: On board the Hindenburg III, Doctor Vargas asks the boy (in German) "Könnten Sie mir bitte versichern, dass dieses Packet überreicht wird". The subtitles translate this as "This parcel must be delivered the moment we reach port". In fact, the correct translation of the German is "Could you please assure me that this parcel will be delivered".
- Revealing mistakes: When the destroyed robot is delivered to the Sky Captain's base, we can see that CGI trucks carrying the robot have no drivers.
- Factual errors: When on his P-40 plane, Captain Sky and his passenger Polly are not wearing headsets. Wind on the fuselage, vibration and engine noise would make it impossible to talk to control tower and they'd have to scream to be heard inside the plane. Yet they speak normally, as if they were sitting in their living room.
- Continuity: In the scene where Joe and Frankie are talking to each other by radio from their "submarine planes," a buzz indicates that its a one way transmission and that they can only speak to each other one at a time. However, a moment later they both say "Protect the rabbits" at the same time.
- Incorrectly regarded as goofs: Captain Sky constantly wears goggles while piloting his plane. In fact pilots of the era were trained to lower their goggles when going into combat to preclude glass or perspex slivers from bullet hits on their canopies from getting into their eyes.
- Errors made by characters (possibly deliberate errors by the filmmakers): Polly is shocked when she wakes up in bed naked with Joe. But she doesn't react at all to seeing Kaji in the bed as well.
- Factual errors: When Joe's plane dives into the sea and converts into a submarine, the force of impact with the water would have surely sheered the wings off.
- Revealing mistakes: When Franky ejects from her plane underwater, no rush of air bubbles escape the cockpit.
- Factual errors: When Dex first tests his ray gun, the reflection of the beams in his goggles travel in the wrong direction.
- Continuity: At one point in the film, Polly takes a flash picture, but her camera contains no flash attachment.
- Factual errors: When Polly sees the reflection of the registration number of Sky Captain's aircraft on the water, the number "h11od" is seen as "polly" from left to right, but in reality it should readable be from right to left (as it would be something like "yllop")
- Revealing mistakes: In the main hangar of Sky Captain's hideout, all the window panes show the exact same damage.
- Factual errors: Headlines in German newspaper shown after the attack of the robots is full of errors. Main headline is "Sehr Grosse Metallic Maschinen Stehlen Stehlen Reserven" which translates to "Very Big Metallik Maschines Steal Steal Reserves". Other headline says "Schlechten Desends Nach Landscape" which means "Bad ??? On Landscape" (the word "Desends" means nothing in German). This line was probably to mean "Evil Descends to the Land" in which case it should appear as "Das Übel kommt in das Land herab". The same goes for Russian newspaper that is titled "Voice People's" and shows headline full of semantical and grammatical errors ("Gigantic Metallic Nation's Reserves Steals Machines Coal, Oil and Uranium. National Leader Attempt To Protect Reserves").
- Audio/visual unsynchronized: In the underwater scene where Joe's "submarine plane" is forced backwards, it makes a sound like an airplane flying through the air.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Revealing mistakes: SPOILER: When Franky gives the order to take the mobile airfield up to ten thousand feet right away, the clouds behind her in the window do not move as they should if the platform had started to rise.
- Errors made by characters (possibly deliberate errors by the filmmakers): SPOILER: At the end of the movie, when Polly lifts her camera to take a picture of Joe, the lens cap is NOT on the camera, even though Joe states that it is after she snaps the picture.
- Errors made by characters (possibly deliberate errors by the filmmakers): SPOILER: On a camera like Polly's, accidentally leaving the lens cap on doesn't mean you've wasted the film. When she blew her shot of Joe at the end of the movie, she could have simply removed the lens cap, cocked the shutter, and tried again.
- Factual errors: SPOILER: Towards the end of the movie, it would be pretty difficult for Joe and Polly to walk around the rocket so easily as its trying to escape earth's atmosphere. And whats more, when the bottom opens up, all the air would be sucked out.
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