The video for "A Year with the Queen" was shown by BBC One controller Peter Fincham at a press launch on Wednesday. It features a clip of the photographer Annie Leibovitz asking the Queen to take off her crown for the shoot, while the following scene apparently showed the monarch walking away, complaining.
However, the promotional clip, which was produced by independent production company RDF Media, was shown in error and the BBC said it was not aware that the clips were out of sequence: the second scene actually shows the Queen walking into the room where the photo shoot is taking place, not out.
The BBC has apologised to the Queen and Annie Leibovitz for creating the impression that the Queen stormed out.
In a statement the BBC said: "The BBC and RDF Television, the producers of the BBC One series 'A Year with the Queen', would like to clarify that the clips shown in a promotional trailer on July 11 were not intended to provide a full picture of what actually happened or of what will be shown in the final programme.
"This was an important photo-shoot prior to the Queen's visit to the United States. In this trailer there is a sequence that implies that the Queen left a sitting prematurely. This was not the case and the actual sequence of events was misrepresented.
"The BBC would like to apologise to both the Queen and Annie Leibovitz for any upset this may have caused."
The BBC Trust has asked Mark Thompson, BBC director general, to include an explanation of how the blunder occurred in his meeting with them next week.
The documentary was filmed as the monarch prepared for her 80th birthday and a visit to the US. It captures the working life of the Royal Family, with clips showing the Duke of Edinburgh, the Prince of Wales and princes William and Harry.
The incident comes just days after the corporation was fined £50,000 over the Blue Peter phone-in error, when 40,000 children phoned in for a competition but a technical glitch meant no winning entrant could be selected, and a girl visiting the studio was asked to pose as the winner.
Leibovitz is best known for taking celebrity shots and earlier this year photographed David Beckham for Disney. However, one of her most famous shoots featured the photo of a heavily pregnant Demi Moore August 1991 for Vanity Fair.