It comes after reports of several people over 40 being turned away from booster vaccine appointments on Wednesday.
Health Secretary Humza Yousaf has encouraged over 40s, who are already eligible for a booster, to move their appointment forward in line with new advice from the Joint Committee on Vaccination and Immunisation (JCVI) that this can be delivered 12 weeks after their second dose.
But several over 40s reported being turned away from vaccination centres, where staff told them they would need to wait for the previous delay of 24 weeks.
Deputy First Minister told Thursday’s Covid-19 Recovery Committee this issue had been resolved, but was accused of being out of touch with the on-the-ground situation, amid continuing reports of the public being turned away from appointments.
Labour MSP Alex Rowley cited a tweet from a woman saying she had been turned away from a centre in Kirkcaldy.
“It's this question about the mismatch between government is saying in this place and what's happening out there,” he said.
Mr Swinney had previously told the committee that this issue, which involved a “limited number of cases” had been resolved.
“I regret very much that some individuals had the experience they had yesterday, because the guidance changed and that should have been applied in all vaccination centres and scenarios,” he said.
“In the light of what emerged in what I’m advised was a limited number of cases yesterday, we have reiterated the guidance to all health boards to ensure that all vaccination centres are operating to that new updated guidance, which of course only emerged at the start of this week.
“But I regret the fact that some individuals were inconvenienced in the way that they were.”
Mr Swinney added that he would “take away” the fresh example of people being turned away.