Fans began leaving Old Trafford with 10 minutes left to play and some of the supporters who remained decided to boo the players at the end of the defeat.
Jones said: "Of course they had every right to do that.
"You can understand that totally, they have had a difficult season. It has not been easy for them, especially here at Old Trafford.
"It's the story of our season isn't it? You win one, but you can't carry the form on. It's disappointing."
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