Jones has signed three contracts at United. The first was when he signed in 2011. The second was in 2015, after averaging 24 league matches in the previous four seasons, which is a very respectable amount for a player who had only turned 23 when he signed it. Here's Louis van Gaal talking about it, at the time:
The third and most recent contract was in February 2019, after averaging 17 league matches in the previous four seasons, and a little over six months after making appearances for England in the 2018 World Cup. That's pretty much half of the league matches during that period, and also bear in mind that just because he didn't make an appearance, it doesn't mean he was injured. He was also an unused substitute and simply not selected for certain matchday squads during that time, which happens to quite a lot of players, seeing as only 11 can be on the field at any one time. Here's Ole Gunnar Solskjaer talking about it:
Why would the club let a player who had averaged over 20 league matches a season and who'd represented his country at a World Cup the summer previous leave on a free transfer? Someone who was happy to play a squad role, who could play in a variety of positions, and who, if sold, would command a reasonable transfer fee? If anything, it would have been daft of the club not to have offered him the contract he signed in 2019. And there was absolutely no reason for Jones not to have signed it when it was put in front of him.