The BBC Trust has upheld three complaints about an edition of Panorama examining the deadly storming of an aid flotilla by Israeli commandos.
A report by its Editorial Standards Committee on the 2010 programme, called Death in the Med, rejected a further 48 complaints.
The committee's chairman said the programme was "an original, insightful and well-researched piece of journalism" despite the complaints.
Israeli commandos boarded the Mavi Marmara, which was part of a flotilla attempting to break its naval blockade of Gaza, in May, killing nine people.
The flotilla was organised by the Free Gaza Movement, and a Turkish group called the Foundation for Human Rights and Freedoms and Humanitarian Relief (IHH).
Following the incident, Israel faced widespread international condemnation.
The committee considered complaints from 19 people about the documentary broadcast on BBC1 on August 16.
The report found two points in relation to accuracy and one in relation to impartiality but said overall it had "achieved due impartiality and due accuracy".
It upheld a complaint the programme should have used material from preliminary autopsy reports to give a "broader picture" of how the activists died.
It also said programme makers should have reflected claims some injured people were mistreated by Israeli forces.
The third point upheld was that the programme should have been "clear and precise" about the nature of the aid on board the flotilla.
Committee chairman Alison Hastings said: "Despite the three breaches, for which the Trust apologises on behalf of the BBC, this Panorama was an original, insightful and well-researched piece of journalism and we commend the BBC for having tackled this issue.
"It revealed important new evidence in a much-publicised story and, overall, the programme was both accurate and impartial. However, these breaches are a firm reminder that the BBC must take great care over accuracy and impartiality, particularly when the subject matter is as controversial as this."
A BBC spokesman welcomed the findings.
He said: "We note that the Trust upheld three out of the 51 points of complaint and we will consider seriously any lessons to be learned. We note that the Trust also remarked it is unlikely that a current affairs programme such as this, covering such a contentious issue, would be found to be entirely flawless if it were subjected to the level of deconstruction and analysis that Death in the Med has undergone."Reuse content