During the third quarter Thomas took his eyes off the ball to run at Reid and bump him. Thomas made strong contact with the Magpie defender, who took no further part in the game.
Collingwood coach Nathan Buckley said the act, which left Reid concussed, was "pretty average".
"It was off the ball and it was unprovoked. We'll see how it settles," Buckley said in reference to the Match Review Panel.
"I think the AFL rules take care of that. I don't want to pre-empt anything but clearly if it is behind play and it is high you're in a bit of strife."
A furious Scott hit back saying Buckley should have held his tongue.
"Commentary like that doesn't help. I don't know what incident Nathan Buckley saw, but a head clash is a head clash," Scott said. "It does happen in football. We play a contact sport.
"'Bucks' should just keep his opinions to himself when it comes to things that will be taken care of by the powers that be.
"It doesn't help when a senior coach comes in and starts influencing things and casting aspersions over our players.
Collingwood players remonstrated with Thomas after the incident and he was loudly booed for the rest of the game.
"From where I sat, it didn't look malicious, and it didn't look like he tried to hurt Ben Reid. But that's not for me to say, and it's certainly not for him (Buckley) to say," he said.
Buckley confirmed Reid would play next week but his words left few in any doubt as to his opinion on the incident.
"It is what it is. It was not a great act and I'm sure he'd be feeling pretty sorry for it right now," Buckley said.
The AFL introduced strict rules in relation to head high contact several years ago that ensured players had a duty of care to their opponents.
A player can be guilty of rough conduct if they make forceful contact to an opponent's head or neck while not contesting the ball.
Peter Ryan covers Melbourne and Collingwood news for AFL.com.au. Follow him on Twitter at @AFL_petryan