When arguing about who is going to steer the torpedoes, a cigar suddenly appears in Charlie's mouth.
When setting the torpedo, Allnut's cigar is shown to be a stub; in the next scene it's longer.
In some close-ups of the African Queen, her name is painted in white letters. Other shots show the name of the boat in black lettering.
When Charlie wakes up in the rain, his blanket is completely soaked. After Rosie lets him in out of the rain, his blanket is dry.
While shooting the first rapids, a close-up of Rose shows her to be sitting with dry clothes. A distance shot shows water cascading into the Queen and all over, either a dummy in the miniature or a stunt double of Rose, nearly flattening her hat. In a return close-up, Rose is still dry, especially her hat.
The propeller on the boat is made of bronze (stainless steel hadn't been invented yet). Bronze cannot be easily welded, even with the proper equipment, but he welds a new blade to the propeller. (In the book, Allnut makes a replacement blade out of iron, and rivets it to the bronze propeller.)
When they are passing the German fort, the Germans and Askaris are using British Long Lee Enfield rifles, not German Mausers.
Flaming wreckage is seen even underwater.
Rainbows don't happen at night.
When pressed for details about the war, Allnust says the "little countries" are involved, naming Austria and Hungary as examples. In 1914, when this story takes place, the Austro-Hungarian Empire was one of the major powers in Europe - the second largest in area after the Russian Empire. In 1918, Austria-Hungary and its allies surrendered and, under the terms of the Armistice, the Empire ceased to exist; Austria and Hungary came into existence as separate nations.
At the beginning of the movie, the deckhands and locals are speaking Swahili yet receive crucial information via African drums. Since, unlike most Bantu languages, Swahili is not tonal, African drums (which depend on tonality) don't work in Swahili. The drums could simply have been used to produce signals rather than language.
When Charlie wakes Rosie, the floor of the boat is dry despite there being heavy rain during the night. This is because the storm occurred further upstream from where they were located.
Katharine Hepburn was a natural redhead in real life but her hair was dyed brown for this film. Yet in the artwork for the original movie poster she is still a redhead. However, as the movie poster is not part of the movie itself, this is not a Goof per IMDB guidance.
Boats float because of the weight of the water that their hulls displace, but the African Queen is an open-topped vessel (no roof), so the boat could not have floated free of the mud and grass just because the rain had made the level of the river rise, since an almost equal "depth" of rainwater would have collected inside the boat as had accumulated on the surrounding terrain. So the boat would have remained at about the same "height" relative to the surrounding terrain, namely, resting on the shallow river-bottom, as it had been before the rainstorm. Charlie and Rosie would have needed to manually pump/bail the boat out before it would float any higher in the river. However, the storm occurred further upstream, causing the river's water level to raise; there was no rain the area where Charlie and Rosie were stuck.
When Rosie tries to climb aboard the boat, it is apparent from her shoulder blade and leg that she is naked. When Charlie helps her into the boat, she is wearing women's underwear.
Several times during the use of the miniature boat, the positions of the figures representing the actors do not match their live action positions.
Due to the non-scalability of water, some of the shots of the African Queen in the rapids and later in the marsh reveal it to be an obvious miniature.
When Charlie and Rosie are being attacked by a swarm of biting flies, the entire swarm moves around in unison. They are superimposed on a glass plate over the film.
While passing the German fort, a hose on the boiler is shot and damaged. Allnut wraps a cloth around the hose and then begins to wrap it with tape. The tape is clearly cotton-based black gaffer's tape, used in movie and stage production to cover and hide set hardware that is not to be seen. Gaffer's tape was invented by Johnson & Johnson in 1942 in response to the military's request for a tape that could be used to seal metal ammunition boxes to keep out water. Thus it did not exist in 1914 when the movie is set.
As the boat pulls into the cove where they are going to bathe, a rope pops up behind the boat as it stops the forward movement of the craft.
When Charlie Allnut gets back aboard the boat after he pulled it with a rope and just after Rose screams because she has seen the leeches on his back, the head of a member of the troupe is visible below the screen.
When Rosy and Charlie are beginning their way down the river after Rosy takes the tiller, a crew member looks over the edge of the boat toward the camera. He is just in front of the canopy at the back of the boat. (Minute 26:18-19)
The nameplate on the front of the church says "1st Methodist". American Methodists sometimes call their churches 1st Methodist, British Methodists never do.
When Charlie shows his map to Rosie, it shows the following names: Hattu, Konna,Talvi and Omena. The names are Finnish and mean Hat, Rogue, Winter and Apple.
After repairing the propeller, as Charlie and Rose are at the back of the boat, the shadow of the boom mic is clearly visible on his white cap.
On the first evening on the African Queen, while Rose is drinking her tea, the shadow of the boom mic appears over the port edge of the boat several times.
At the end of the leech scene, the boom mic is visible for a split second at the bottom of the frame.
When Allnut goes underwater to check the propeller, the water lifts up the back of Humphrey Bogart's toupée, revealing his bald pate.
When Allnut is telling the Reverend and Rose about the war, among the countries he says are involved in it is Spain. In fact, Spain was never at war throughout the 1910s.
Charlie at one point in the journey taunts a pod of hippos. Anyone who knows Africa as well as Charlie supposedly does would never do that as hippos are extremely dangerous and have been known to attack boats with little provocation.
Robert Morley's character refers to a college friend slightly younger than him being made a bishop. American Methodists have bishops, but British ones don't.
The torpedoes that Charlie made for the African Queen were constructed from red hydrogen cylinders. He said they were oxygen cylinders, which are black.