Revealing mistake: When the boat is supposedly surrounded by a swarm of flies, they're really just relatively few flies trapped between two panes of glass in front of the camera lens. Evidence: whenever the camera moves, the "swarm" moves with it against the background, and you can even see some of the insects walking on the surface of the glass.
Continuity mistake: When Charlie Allnut grabs a bottle of gin from the box, all the bottles in it are wrapped with paper for transport. But when Rose Sayer takes the bottles out of the box to empty them into the river, the paper is gone (from the movements of her hand/wrist, you can tell that she doesn't unwrap the paper from the bottles).
Continuity mistake: In the scene where there is a terrific storm while Bogart and Hepburn are asleep, Bogart gets extremely wet before being invited into the shelter by Hepburn. Upon entering the shelter and lying down to sleep, Bogart's blanket is perfectly dry.
Factual error: In the scene where the German East African troops are shooting at Bogart and Hepburn, their rifles are Gewehr 88 "Commission Rifles'" with five-shot magazines. In actuality, the German East African troops, under the command of Colonel Paul Von Letow-Vorbeck, were equipped with the absolute dregs of the Kaiser's arsenal: Gewehr 71 single-shot rifles, and Gewehr 71/84 8-round tube magazine rifles whose magazines usually got fouled and had to be used as single-shot rifles anyway.
Revealing mistake: When Charlie and Rosie are on the river underway, and Charlie is done mimicking animals like the hippos and chimps, they snuggle in the back of the boat, which is chugging along. The viewer has a clear shot of the water behind the boat - which has nary a sign of wake.
Factual error: The scene where the German officer is blinded by the sun and thus can't shoot at Humphrey Bogart could never have happened. The Imperial German East African Army had no rifles capable of accepting a telescopic sight. In fact, throughout the war, its commander, Colonel Paul Von Letow-Vorbeck, had his marksmen trained to use open sights, not scopes. The rifle used in the scene was a British Lee-Enfield No. 1 Mk. 1 modified to accept a telescopic sight, which would have been scarce in Africa, even in the British Army. But it couldn't have been captured, as unit armorers in the British Army began scoping Lee-Enfields in mid 1915.
Factual error: During the last scene, after the German gunboat sinks and the two main characters are thrown into the lake, both Bogart and Hepburn are swimming toward the shore of the lake. Even though there is nothing which could reflect the sound of the two swimming and splashing water, one can hear the echo of water splashing. Apparently, the last scene was filmed in a pool on a sound stage.
Continuity mistake: In the scene where Humphrey Bogart and Katharine Hepburn are taking a bath in the river, Katharine starts off looking as if she is bathing fully undressed. As she climbs into the boat, however, she is clearly seen with a full set of underclothing that includes shoulder straps which were not there earlier.
Continuity mistake: When Rose and Charlie are getting married on the Louisa, one camera view of the couple shows a small island in the background, about 50 yards off the port side. The island stays in the exact same place in all subsequent shots from that angle, indicating that the ship is stationary. When they cut to shots looking towards the bow of the Louisa bearing down on the capsized African Queen, it is traveling at a good pace, as evidenced by the bow wake.
Continuity mistake: When the African Queen finally passes the fort, in the final few seconds you can see somebody standing in the back of the boat. Both Charlie and Rosie are still crouched down low in the next shot.
Revealing mistake: In some parts of the movie, the boat used is diesel powered. In one particular scene the viewer can plainly see the diesel exhaust from down low on the stern as well as small wakes on the surface of the water from the exhaust passing above it.
Revealing mistake: Charlie calls Rose to take the tiller, for the first time. She has a hamper on her lap, but there's nowhere to put it, so she takes it out and lowers it down below the bottom of the screen, then she takes her hands away and the hamper quickly disappears. Some crew member must have taken it away.
Revealing mistake: In the scene where Bogart and Hepburn are in a boat cruising down the river and laughing at some monkeys or apes on the riverbank, in the medium close-up shots of them together you can see glow and signs of matte and chromakey shining in their hair. (00:59:00)
Revealing mistake: When the explosions on the Louisa happen, towards the end of the wider shot you can see the actors stopping any reaction (Charlie pulls the head out of the noose and then just looks at Rose without moving an inch closer, and Rose herself keeps her arms down all the time without even attempting to free her neck), just waiting for their cue to do other actions in other takes. (01:42:45)
Revealing mistake: As Charlie holds Rose close and tells her that "We'll never lack stories to tell our grandchildren" after the assault of the bug swarm, the background is perfectly in focus, but the engine behind them is not - on top of showing chromakey white noise in the top right corner. (01:13:35)
Revealing mistake: When the protagonists get suddenly attacked by the mosquitoes, those appear and disappear completely randomly like in an on/off switch, both times when the boat is supposed to move very slowly or even not at all (they appear when the boat is anchored). Moreso, even if the boat is anchored, the background behind Bogart and Hepburn keeps scrolling, and when Mrs. Hepburn swats the flies away yelling "Charlie!", the contour of chromakey screen is visible. (01:10:55)
Continuity mistake: Rose offers Charlie to help with the propeller. He says "Here goes" and motions to go back underwater. Katharine Hepburn's hands are on the vertical supports sticking out. Not a moment has passed (you hear the plop of him actually submerging) and in this new reverse shot her hands are by those same supports, not on them. (01:07:15)
Revealing mistake: Before the boat gets into the steep rapids following the bit with Allnutt doing hippo and monkey impressions, the wide shot shows the mannequin supposed to stand-in for Bogart all bent over in a way that does not mirror the actor at that point (but fits the bit when the boat is taking a nosedive). (01:02:40)