The manager thinks the versatile defender, who has enjoyed a tremendous start to 2013, should be in Roy Hodgson's senior party for the friendly against Brazil at Wembley.
Despite press reports that United are unhappy at the prospect of Jones playing in the European Championship in the summer for Stuart Pearce's side, Sir Alex understands the situation.
"I haven't paid much attention to it," he admitted at his pre-Fulham press conference. "I'm surprised he's in the Under-21s and not the full squad.
"I think it's happened quite a few times to players [being dropped back to Under-21s]. Is it understandable to the players? That can be the difficult thing to manage. The players, once they're in the full squad, think they've achieved that - he's played for the full squad.
"If they then take a step back, it can be hard to manage that. But he's 20 years of age and Stuart Pearce wants to pick as good an Under-21 squad as he can get. And that includes players like Phil Jones."