With his side 2-0 up at the Britannia Stadium, Stoke defender Wilkinson received a booking in the third minute of stoppage time for bringing down Dembele, who clutched at his left leg and had to be carried off on a stretcher.
The Belgium forward departed the stadium on crutches and Cottagers boss Hughes - who recently lost striker Bobby Zamora to a broken leg - was left fuming.
"If he (Dembele) has avoided serious injury then he has been a very lucky boy because the tackle that took him out was, from my point of view, an absolutely ridiculous challenge at that stage of the game," Hughes said.
"When you are at that stage of the game and your team is leading 2-0, there is a certain code, I would suggest, that you look after your fellow professional, and the lad has ignored that.
"There was no need for the challenge at that late stage in the game and he has put a fellow professional's career at risk by the nature of it. I don't know what the hell he was thinking about to be perfectly honest."