Continuity mistake: When Munchausen is about to be executed for the second time, right after the Sultain sais: "Executioner, execute!" we see the executioner raising the axe. The axe is facing the wrong way. In the next shot it's the right way. (01:39:45)
Visible crew/equipment: In the scene after the storm, the ship moves in the sand. Look at its front and you'll be able to see a wire that moves the ship. It's very visible.
Visible crew/equipment: When they're building the petticoat balloon, the camera slowly goes back. Look at the lower-right corner of the screen: there is a man wearing a stadium jacket. He's a crew member.
Visible crew/equipment: When Vulcan is taking away Baron, look carefully and you'll be able to see a wire in the tail of his coat.
Deliberate mistake: Baron Munchausen sends his courier, Berthold, on a one-hour errand to procure a bottle of the finest Tokay from the imperial wine cellars in Vienna. Berthold returns with the bottle within the hour and (in one continuous wide shot) hands the bottle to Baron Munchausen, who then hands it to the Sultan, who effortlessly plucks the cork from the bottle with his fingertips and pours a glass for himself. But there is no way the Sultan could simply pluck out the cork with his fingertips in one move; this extremely valuable bottle of wine is visibly sealed (in every shot) with a thick, air-tight red wax. This wax must first be cut and peeled away to access the deeply-embedded cork, and the cork must then be removed with a wine key (corkscrew). The action of properly opening the bottle would have required more time than the entire scene itself; so, to expedite the flow of the shot, director Terry Gilliam deliberately chose to forego a proper uncorking.
Suggested correction: You're ignoring the fact that the entire scene is a story the real Munchausen is telling from memory. There are many fantastic elements that do not hold with reality, like him riding his horse out of the window, falling several stories, and landing safety, or Adolphus being able to see and shoot to the other side of the world. The bottle is simply an example of Munchausen not adhering to reality.
In any event, the Sultan's effortless uncorking of the bottle was a deliberate mistake intended to allow a whole series of actions to occur sequentially in the single wide shot in less than 5 seconds.
Yet, at the end, Sally addresses Baron Munchausen directly and asks him the question that the audience has been wondering throughout the whole movie: "It wasn't just a story, was it?" The Baron solemnly shakes his head, affirming that he was telling the truth all along, regardless of how fantastic it sounded. This point is often missed by the movie's critics.
The point I raised wasn't that the Baron's story wasn't true, but rather that he embellished it.