During the treasure of Collie Baba sequence, when Scrooge orders Dijon to bring their sacks, his "treasure-hunting" outfit briefly returns to his trademark waistcoat.
During the climactic infiltration of the money bin, the nephews shut down all the alarms. Later, however, when they are seen running up the stairs toward Scrooge's office (when the bin is being transformed into Merlock's fortress), an alarm is going off.
While the genie is talking to Huey, Dewey and Louie about Merlock, in one shot, Huey's shirt is shown as a dark shade of red despite the fact that it should be lighter.
When Merlock puts his talisman on the lamp, the lid is missing. A few minutes later, when the nephews get the lamp away from Merlock, and his talisman falls off, the lid has reappeared.
The expedition is shown riding Bactrian (two-hump) Camels, but these are only seen in Central Asia, not the Middle Eastern setting of the movie. This does, however, allow the joke of the nephews riding a three-humped camel.
When Scrooge scolds his nephews, Webby, and the disguised Genie, there are two Louies walking up the stairs.
In the cave of Collie Baba, Launchpad sets off the booby trap that shoots out fire, yet he never steps anywhere near the button that triggers it.
When Scrooge opens the treasure trunk of Collie Baba's clothes, you can see that the cels of the trunk are not properly lined up when Webby ducks the lid.
As the shadow of an owl flies over the Genie when he is laying in bed, it freezes in place right at the bottom-left edge of the camera, indicating that the animators stopped animating too soon.
When we get a full view of Huey, Dewey, and Louie on the camel, the camera pans out to reveal everyone else on camels. As it does so, Scrooge and his camel suddenly pop in out of nowhere.
At the end of the film, Merlock is seen falling to his death after losing his talisman. However, it is mentioned earlier in the film that one of his wishes was to live forever, which means this is not possible.