When Shirley is out with Joy giving their dolls buggy rides and Joy wants to operate on Shirley's doll, Shirley says she doesn't want Mary Lou to be operated on. But the doll she actually has is not the small one she named Mary Lou, it's the larger one named Lupee given to her by the aviators.
When the man in the convertible offers Shirley a ride to the airport, she is wearing her aviator hat. But when she climbs into his car, her hat is gone.
At the very end of the movie when Uncle Ned reveals who got Shirley, Joy is holding her hands in front of her. When the scene moves into Joy, her arms are crossed.
During the song "On the Good Ship Lollipop" while the plane is taxiing you can see the edge of the screen where they are projecting the outside. This is most obvious when she sings the line "...and there you are..." just after "Cracker Jack Bands fill the air" the first time.
As Shirley parachutes to earth with Loop Merritt, her hair is unaffected by the wind, and remains perfectly in place (although it blows all over once they land in the storm).
At the end of 'On The Good Ship Lollipop' on the plane, the men join in on the singing. The blonde man directly behind Shirley is mouthing off-note, as if he forgot the words.