A video emerged that appeared to show the US president refusing to shake the boy's hand at the White House.
"How stunning, and how horrible, that Trump cannot bring himself to shake the hand of a small boy who only wanted to touch the president," the author said.
But Marjorie Kelly Weer, mother of Monty, said Rowling's interpretation of the clip was wrong.
The Harry Potter author tweeted: "Re: my tweets about the small boy in a wheelchair whose proffered hand the president appeared to ignore in press footage.