A 3-0 defeat at Port Vale on the final day extended United’s winless run to seven games – with only rock bottom Macclesfield Town below them in the npower League Two’s form table during the run-in.
It saw the U’s blow a four-point cushion over Crewe Alexandra, whose 16-game unbeaten run saw them finish four points in front to set up a play-off semi-final against Southend United.
Thomas, who felt performances earlier in the season were worthy of a side heading for automatic promotion, was dejected with the way the season panned out.
“We’re all disappointed with the way we’ve finished and (against Port Vale) we went out with a bit of a whimper, so we’ve got to put that right,” he said.
“This is a setback really and we’ve got to see how we come back from it.
“We’ve got to find some stronger players who can finish the season off better.”
The U’s chief stressed it was important not to over-react and did not expect wholesale changes to the playing staff during the close season.
Thomas will be meeting manager Chris Wilder this week to begin the task of learning from the season to make sure improvements are made in time for the new campaign.
He said: “We’ve got to be fitter and stronger.
“We’ve had too many injuries and we’ve got to look at the department as a whole, from the playing side and look at how to improve.
“I think over the last seven or eight games the performances haven’t been terrible, but we haven’t scored when we needed to and I don’t think we’ve finished strongly enough, that’s plain to see.
“We are low and hurting as a football club. But we will be positive, this isn’t a case of clearing everything out and starting again.
“We’ve improved on last season – not by enough – but we have to use those experiences to get better.”
l Port Vale v United match report: Pages 38-39 l More reaction: Page 37 l The four games United will rue: Page 36