The 21-year-old missed the first three months of Manchester United's title-winning campaign with back and knee problems.
And, after winning praise for his man-marking job on Cristiano Ronaldo in United's Champions League tie at Real Madrid, an ankle injury ruled him out of the return leg at Old Trafford.
That damage was done in a challenge with Reading's Jobi McAnuff, and Jones said: "It was a silly tackle.
"I probably should have looked after myself a bit more. I will learn from it as an experienced head would probably not have done that. It is in me. I like making tackles. I like defending.
"I was gutted to miss the Real second leg. I tried everything to make the game.
"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 I think I've done reasonably well towards the back end of the season."