Two quick-fire headers from Jake Sinclair had cancelled out Jesse Lingard's early opener to put Saints in front with 20 minutes left to play at Altrincham's Moss Lane ground.
But United hit back through Larnell Cole and Frederic Veseli to restore their advantage before Calum Chambers made it three-all with the last kick of the game.
Hunter praised his players' resilience after trailing twice at either end of the match, but admitted his emotions were clouded by the fact his side squandered a winning position of their own.
He told Saints Player
: "I'm actually disappointed we've not won the game.
"We said to the players at half time that this was a proper game of football against very good players – Manchester United are a great test – so we put one-or-two things right, particularly the disappointment of a very slow start and going a goal down inside three minutes.
"There was a good response from that but, having then scored two really good goals, to concede two more is not what we're about.
"This epitomises the type of game and opposition we want to be playing to test ourselves and see how good our young players are, so it's disappointing.
"We've had a few words at the end of the game and we'll move on.
"It should never have got to that situation, but fair play to Calum," Hunter said of Chambers' last-gasp equaliser. "He's back in central midfield and that's a good strike to beat the 'keeper.
"The players can play at the tempo we want them to, though there are still rough edges we need to knock off them.
"They were shattered in the dressing room because of the physical nature of the game and the way the ball gets transferred about in top-class football.
"But, at this age, it's about winning and seeing games out because they are on the verge of being senior players."