The Beatles spot five Apple Bonkers taking apples off a tree. Only four Bonkers march and sound off before a Meanie Squad Leader.
In the beginning when the Chief Blue Meanie is holding up Max and scolding him, the colors/stripes on Max's boots switch back and forth a couple times.
Paul and George's shirts change colors throughout the movie. Paul's shirt varies from a more purplish hue to an almost-black hue, and George's shirt varies from a greenish-brown to a more orangey-brown.
The yellow submarine sometimes have twin propellers and sometimes a single propeller.
When Fred starts tossing aside the pile of apples covering the Lord Mayor, apples materialize in places where they had been removed.
At the end of the "Sgt. Pepper's Lonely Hearts Club Band" number, the next singer "Billy Shears" is introduced. On screen Paul, George and Ringo all indicate that John is going to sing next and point to him, but the next song in the film is the same as on the album, "With A Little Help From My Friends", with vocals by Ringo.
When Fred is carrying the Lord Mayor and running, he appears to step on a bush instead of running behind it (layer mistake).
One of the tag lines for the film is "Nothing is real," but "Strawberry Fields Forever" is not used in the film itself, nor is it on its accompanying soundtrack.
Just before Ringo pulls a lever, he says that he is a "born lever-puller," a joke on the Beatles being from Liverpool. However, the proper term for a citizen of Liverpool is Liverpudlian.