Problems with his back and then knee meant Jones did not make his first appearance of the campaign until November and having subsequently seen fairly regular action up to February, he then damaged his ankle tackling Reading's Jobi McAnuff in an FA Cup tie.
That injury kept the versatile 21-year-old, praised for his efforts in shackling Cristiano Ronaldo during the Champions League last-16 first-leg against Real Madrid, out of the return leg, in which United were eliminated.
It has all made for a testing time for Jones - who is satisfied with how things have gone following his comeback in April, with United since securing the Barclays Premier League title - and he has vowed to learn from his experiences this term.
The England international told the Red Devils' official club magazine Inside United: "It has been frustrating. Certainly at the start of the season.
"It was tough as I had a back injury and then, in the first or second training session back, I injured my knee again.
"It was kind of one thing after the next and I felt like 'is this sort of thing going to end?'
"Thankfully, I got over that and played in quite a few games and cup games as well.
"The cup ties really gave me a chance to have more game-time and I think I've done reasonably well towards the back end of the season."