Despite this, the outgoing Director General of the BBC claimed that the programme was for the most part "a really good piece of broadcasting".
BBC News reports that while Thompson conceded that there were some flaws with the coverage, with "one or two - not many but one or two - inaccuracies in the commentary which we shouldn't have had", he also pointed out that the audience approval ratings on the whole had been high, remaining "above eight out of ten" across all four days of the broadcast.
Thompson refused to "talk about individual elements" of the coverage, despite being repeatedly quizzed by MPs on a segment where Fearne Cotton and Paloma Faith discuss a Jubilee memorabilia sick bag.
Cotton recently described the critics of her presenting during the Jubilee as "bullies'.
The coverage was criticised by a number of high-profile presenters, including Stephen Fry, ex-Woman's Hour presenter Sue MacGregor and Jonathan Ross, who described it as "p*ss-poor".
The programme also resulted in more than 4,000 complaints from the public, centred primarily around the segments depicting the river pageant.
Thompson was making his final appearance before the House of Commons Culture Select Committee before he steps down as Director General later in the year.
The 54-year-old added that he is hoping for a quick transition, hoping that "the handover [will] happen sooner rather than later".