Moyes was sacked as United boss on Tuesday, just 10 months into a six-year contract.
One highly-placed United source said the board started worrying about Moyes' ability to get the best out of his players during the February defeat at Olympiacos.
"The players didn't seem up for it," the source said.
Moyes was dogged by rumours - always denied by the Scot - that he did not get on with a number of his players.
But Jones denied claims the squad simply stopped playing for their former manager.
"That was never the case," the United defender said.
"Players don't go out on the football pitch to lose games. That is ridiculous.
"Everyone wants to win every game at this club. That accusation is hurtful.
"It's not happened for whatever reason but we need to move on quickly and end the season well."
Moyes made no mention of his playing staff in the statement he issued following his dismissal, and the United players remained mysteriously quiet on social media channels earlier this week.
But Jones insists the United squad were sad to see the former Everton manager lose his job.
"On behalf of the lads we thank David Moyes for the work he put in for us all," the England defender said.
"He is a nice man and we wish him all the best.
"We are sorry he has lost his job and probably we didn't get some of the results that we would have liked to for him but that's football."
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- David Moyes