The trio alleged that Mr Patel's group website links to Holocaust denial material. They also claimed he had previously said the September 11 terrorist attacks were caused not by Islamic fundamentalists, but by the CIA and Mossad.
Mr Patel denies all the allegations against him.
But viewers were unable to see their discussion after a satellite failed and the live show, presented from Leicester by Nicky Campbell, went off the air.
The BBC said it was also unable to upload the programme to its iPlayer service because of the "technical difficulties" which rendered the programme "incomplete".
Mr Patel had been on the Mavi Marmara boat when Israeli commandos boarded it and clashed with activists. Nine of his shipmates died.
Friends of Al Aqsa describes itself as a "non-profit making NGO concerned with defending the human rights of Palestinians and protecting the sacred al-Aqsa Sanctuary in Jerusalem".
Mr Hoffman said: "On the website there are links to Holocaust denial material. This was pointed out by Rabbi Schochet on the show.
"Martin Stern has been to lectures Mr Patel has given to students where he has said Islamic fundamentalists did not cause 9/11 and blamed the CIA and Mossad.
"When Nicky Campbell asked about the 9/11 issue Mr Patel denied it. But Martin said 'I'm sorry, but I was there and you said it'. That blew the credibility of his flotilla testimony."
Mr Hoffman criticised the BBC's failure to provide the show online: "At a time when the people who were on the boats are speaking in public, here is an example of someone whose testimony is completely unreliable and no one will see the programme. It has to be put in the public domain."