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.
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.
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)
Continuity mistake: During the conversation on the porch that follows Samuel Sayer's death, Katharine Hepburn is obviously lit differently depending on the camera angle; in close-ups her chest is fully shadowed, while in the wider angles (with Bogey in frame or not), light reaches the first button of her dress. (00:17:25)
Continuity mistake: After the death of her brother, Katharine Hepburn is sitting on the porch. The knitting kit on the table is showing some blue fabric peeking off the lid, and there's a reel next to it. In the close-up that follows, white fabric is showing (the blue one is on the opposite side, barely visible) and the distance of the reel has changed. (00:16:20)
Continuity mistake: The reverend shoves aside a German officer and gets smacked in the face with a rifle. Robert Morley sports heavy blue makeup, a not-so-believable instant ecchymosis. In the next scene the village ruins are still smoking, but his face is clean; the bad bruise and little cut on the lip have vanished without a trace. (00:12:00)
Continuity mistake: The reverend and his sister get on their knees to pray for England as Allnut leaves with the news of war. Reverend Sayer has his jacket unbuttoned; hearing the shout from the villager announcing the Germans' arrival, his blazer is suddenly buttoned up when he rushes to talk to him. (00:11:00)