The 16-year-old featured in the match against their Premier League rivals as part of their tour in Australia.
The game ended in a 1-0 victory for Steven Gerrard's side at the Suncorp Stadium in the Queensland Champions Cup.
There was not too much 'friendly' about this match, though, and a particularly crunching tackle from McGinn left those connected with Leeds outraged.
The midfielder closed down Gray as he looked to pass the ball. Although he won the ball, he went in with his studs up and caught the teenager on the ankle.
Gray was put on a stretcher and taken off the pitch, with McGinn appearing to apologise to the player.
Leeds boss Jesse Marsch said: "We're hopeful that it's not too bad. He was in some pain initially but we're hopeful nothing is broken.
"Hopefully it's an ankle sprain and we'll see the severity of it in the next couple of days."
Gerrard defended McGinn following the incident, saying: "We wish the young kid very well, hopefully it's not a long injury. John's got the ball, he's been unlucky in the follow through.
"There was one just before by the same boy on (Emiliano) Buendia and my heart was in my mouth.
"In the main it was played in the right way. It got feisty for a short period, there were a few feisty tackles from them, a couple from us.
"You've got two Premier League teams who want to win a game. Both sets want to win even though it's a friendly. It's normal."