Pakistan-born Rafiq, 32, first went public with allegations of racism and bullying in September 2020, related to his two spells at Yorkshire County Cricket Club.
He had informed Yorkshire's initial 2021 probe that Vaughan had told Rafiq and three other players before a match: "There's too many of you lot, we need to do something about it."
But during the second day of a Cricket Discipline Commission hearing, Vaughan's lawyer referred to a Wisden interview in which Rafiq quoted Vaughan as saying: "There's too many of you lot, we need to have a word about that."
Rafiq said the second version was the one he remembered, adding: "In terms of the statement, there was a clear mistake and I take full responsibility.
"I want to emphasise it is very clear on 'too many of you lot' which is the discriminatory part against a group of Asian players. The second part is an action. Clearly, there is a discrepancy."
Questioned by Vaughan's lawyer, Christopher Stoner, over why a discrepancy existed, Rafiq replied: "I have no explanation at all." Asked how he knew it was Vaughan who made the alleged comment, Rafiq replied: "I know what his voice is like."
He was also asked about a November 2021 meeting at which Rafiq said Vaughan offered an "apology non-apology".
"Michael headed off to Australia and his general chat around all this was relayed back to me," he added. "I felt like I was being played."
ECB lawyer Jane Mulcahy had earlier repeated the allegation Vaughan made the "too many" remark on the outfield before a Twenty20 match between Yorkshire and Nottinghamshire at Trent Bridge on June 22, 2009.
The players concerned were his Yorkshire teammates Rafiq, Rashid, Rana Naved ul-Hasan and Ajmal Shahzad.
Mulcahy said the ECB (England and Wales Cricket Board) contends Vaughan made the alleged comment and therefore "caused prejudice or disrepute to cricket".
Rashid was called as a witness via a video link from Bangladesh, where he is playing in a one-day international series for England.
He reiterated to the CDC his belief that Vaughan's comment was a "poor attempt at humour", adding the 2005 Ashes-winning skipper was "not racist" in his view.
In over an hour before the CDC panel, Rashid also insisted he had a "very clear recollection" of Vaughan's alleged remarks.
Rafiq told British lawmakers in December 2022 the abuse he and his family had faced had forced him to leave the UK.
Vaughan and fellow former Yorkshire players Matthew Hoggard, Tim Bresnan, John Blain, Andrew Gale and Richard Pyrah all face charges related to the use of racially discriminatory language.
Stoner confirmed Vaughan, 48, denies the charge and said the burden of proof was on the ECB. He added Vaughan's autobiography made it clear having four Asian players in the team was "good for Yorkshire cricket".
Stoner stressed the allegation was "not in fact mentioned by anyone for a period of 11 years". "Now, 14 years after the event, it is word against word."
Vaughan, due to give evidence on Friday, is the only one of the cricketers charged by the ECB over bringing the game into disrepute set to attend the hearing.
The ECB brought charges against seven individuals, and Yorkshire, in June last year. Another player, Gary Ballance, has already admitted a charge related to the use of racially discriminatory language.
Ballance, a former England Test player, is now playing for the country of his birth, Zimbabwe. Yorkshire have also admitted four charges.