Extent of striker's injury is not yet known...
Hughes already has Bobby Zamora ruled out for the majority of the season with a broken leg and was incensed by Wilkinson's reckless challenge on the Belgian in last moments of the tie.
"We will know in the next 24 hours how bad the injury is, but if he has avoided serious injury to his left leg, he's a lucky boy," Hughes told Sky Sports.
"The tackle which took him out from my point of view was a ridiculous challenge at that point of the game.
"At that stage of the game when you're leading 2-0, there's a certain code that you look after your fellow professionals. The lad has ignored that and there was no need for a challenge like that.
"He has put a fellow professional's career at risk and I don't know what the hell he was thinking of.
"Hopefully Moussa has been fortunate. If there's no break it's a blessing because at the time I thought he had a real serious injury."
Wilkinson was booked for the challenge by referee Mark Halsey and Stoke City’s assistant manager, Dave Kemp, conceded the defender did not need to make such a tackle so late in the game.
"It was an unnecessary, rash challenge," said Kemp.
“We are football people too. There was no malice in the challenge, just over-enthusiasm. We've spoken to Andy about it and he didn't need to make that tackle. We just hope the player has not been badly hurt."
Dembele's injury means Hughes is another striker short, although the extent of the damage to the striker has not been confirmed.
Stoke progressed through to the last 16 of the League Cup with a 2-0 win, courtesy of headers from Danny Higginbotham and Kenwyne Jones.