Throughout the movie, Jimmy Page and John Paul Jones have different outfits on. However, this is because the movie was filmed when the band played Madison Square Garden 3 nights in a row in 1973, and both Jimmy and John Paul didn't want to wear the same outfits. Small portions of songs were also filmed in 1974 at Shepperton Studios because of missing pieces of songs.
Right at the end of Whole Lotta Love, there is a camera shot from above the band, over the stage looking down. John Paul Jones can be seen removing his bass guitar and putting it on a horizontal surface. Then the camera cuts to a front shot, as seen from the audience and Jones still has his bass guitar around his neck.
Near the end of "Dazed and Confused", during the camera-spin, Jimmy Page can be heard soloing wildly in high-note arpeggios for which his fingers should be closer-to-the-body (his AND the guitar) but the footage shows clearly his left hand up closer to the headstock in chord-strumming positions. During the same song there are obvious footage inserts where he is not as sweaty as he appears in clips preceding, following, & throughout the rest of the song.
During the intro to Stairway to Heaven when John Paul Jones is shown playing the flute part on a keyboard (right before Robert Plant's first vocals) , the movements of his hands do not match the music. Particularly notable are that early in the shot, his hands are completely off the keyboard while several notes are being played, and near the end, his right hand (the only one playing notes at the moment) is moving to the right, which would generate ascending notes, but the music is descending.
When Peter Grant, the band's manager, is pretending to be a 1930's gangster, two different vintage cars are used in the same sequence. This is most visible by the cars' hood ornaments.