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.
"Multiple sources have informed me that that was not a full or accurate representation of their interaction.
"I very clearly projected my own sensitivities around the issue of disabled people being overlooked or ignored onto the images I saw and if that caused any distress to that boy or his family, I apologise unreservedly."
Rowling didn't apologise to Mr Trump himself.
Mr Trump is said to have shaken the boy's hand as the president entered the room.
Ms Weer wrote on Facebook: "If someone can please get a message to JK Rowling: Trump didn't snub my son & Monty wasn't even trying to shake his hand."
She also said her son was not all that keen on shaking hands anyway.
Rowling has deleted her initial tweets on the subject.