Revealing mistake: When the spice filled tank carrying the mutated Guild Navigator enters the hall where the Emperor is waiting, one of the Guild agents falls to the ground at the left side of the tank; first an arm trying to stop the fall and then the head are visible for a moment. (00:06:15)
Revealing mistake: In the extended version, when Dr. Yue receives the message from Baron Harkonen, one of the "dead" bodies in the background can be seen moving. (01:00:55)
Revealing mistake: During the invasion of Dune by the Harkonnen, a Sardukar soldier throws a guard from what appears to be the palace's wall. When he hits the ground all the bodies around him bounce as if they where lying on some sort of cushion. (01:09:50)
Answer: Because it was edited in a way he didn't approve of. The film was actually over 3 hours long, and it was trimmed by about an hour for the cinema version, and then a certain amount of pick and mix went on to come up with the video version.
David Mercier