The Red Devils defender, along with Arsenal winger Alex Oxlade-Chamberlain, were singled out by former boss Stuart Pearce as two players who did not make themselves available for the Young Lions at this summer's U21 European Championships in Israel.
But Jones, who is an eight-time capped senior international, has denied those claims saying he would have played if called upon.
"I didn't expect it and I am disappointed," he said of Pearce's comments.
"It is simply not true. I have represented the Under-19s, the Under-21s and the seniors. I said from the first day I pulled on an England shirt, it sent shivers down my spine.
"How he can come out and say I didn't want to play for the Under-21s is beyond me.
"It wasn't nice to read what he said and I am sure Alex Oxlade-Chamberlain is thinking the same thing."
He added: "It was totally out of my hands.
"Roy Hodgson came out prior to the Under-21 tournament and said he regarded me as a senior player.
"I went on to play against Ireland and Brazil, so it wasn't a waste of time going with the seniors.
"It hasn't dampened my enthusiasm for England though, definitely not. It is an honour to represent your country at any level."