The party accused former Sun and BBC reporter John Ware of being biased.
In one of those cases, Labour claims the program deceptively edited the content of an email sent by Milne to change the meaning.
This polarisation - which I've long argued is the result of both ends of the debate trying to force the issue of antisemitism through the prism of Jeremy Corbyn as an individual - is part of the reason that the problem has been such a protracted one.
It is no longer enough to issue a few angry tweets or to tell people like me privately that they understand why we left the Labour Party or that they disagree with Corbyn and the people around him.
Mr Hogan alleged the people Ms Formby had hired "overruled us and downgraded what should've been a suspension to just an investigation or worse to just a reminder of conduct, effectively a slap on the wrist".
Iain McNicol also spoke out against the party on the programme.
"I've been told by a general secretary that I'm not legally responsible for dealing with outside regulatory bodies", Watson said.
Meanwhile, former head of disputes, Sam Matthews, said he interpreted an email from Mr Milne as "not a helpful suggestion" but as "an instruction".
The BBC reported that, in the email from March past year, Mr Milne said there should be a review of the disciplinary process into anti-Semitic complaints. - What the BBC didn't report is that the communications chief had been asked his opinion on a case of a Jewish Labour member, with a Holocaust survivor parent who was yet being accused of antisemitism.
"We completely reject any claim that the Labour Party is anti-Semitic", the party said in a statement.
The BBC quoted an email from Milne telling Labour's internal complaints team that "something's going wrong, and we're muddling up political disputes with racism".
A Labour spokesman accused the broadcaster of "pre-determining" the outcome of its investigation.
Labour said the accusations were "deliberate and malicious misrepresentations created to mislead the public".
"Labour is taking decisive action against anti-Semitism, doubling the number of staff dedicated to dealing with complaints and cases".
Panorama spoke to former party officials, who alleged they had to deal with a huge increase in antisemitism complaints since Jeremy Corbyn became Labour leader in 2015.
"This throws into doubt their credibility as sources".
Labour has denied the accusation and stated "the rate at which anti-Semitism cases have been dealt with has increased four-fold" since Ms Fromby's appointment in 2018.
Speaking to BBC Radio 4's Today programme on Thursday, Watson urged Corbyn to immediately introduce changes including automatic exclusions and said he was the only person who could tackle the problem.
Labour members have even been arrested on suspicion of racial hatred and the party now faces a full official inquiry for racism by the Equality and Human Rights Commission. A 2015 Panoramaepisode Ware produced on Corbyn made false claims and was widely denounced as a "hatchet job", while a 2005 program Ware produced about British Muslims was slammed as "McCarthyite" and "disgusting" - the latter by a former Panorama journalist.
"An honest investigation into antisemitism in Labour and wider society is in the public interest. Very serious questions now have to be answered". "It is a very partial view from a few members of staff who have a political axe to grind", he said.
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