Oliver failed to point to the spot in the second half of the New Year's Day clash at the Britannia Stadium despite a clear Chris Smalling handball.
Hughes also felt Stoke should have been awarded a penalty for a foul on Geoff Cameron soon after.
"We had two penalties in our view not given," he told Sky Sports after seeing Radamel Falcao cancel out Ryan Shawcross' early opener.
"The obvious one was Peter Crouch. He headed towards goal and it's an unnatural movement from Smalling.
"It's a clear penalty and I have no idea why the referee hasn't given it when he is three or four yards away. He needs to be stronger.
"And when Pete has headed against the post, you can see Geoff Cameron is about to put it in and he gets taken out."
Hughes felt an opportunity to convert a winner would have been just reward for Stoke's performance.
He added: "We're disappointed. In terms of chances created, pressure and momentum, we were the team that was most likely to score.
"We have come up against a good team and I think on the day we were the better team. That shows how far we have come."
Hughes also moved to deny newspaper rumours linking Peter Crouch with a move to West Brom, insisting the striker's future remains at the Britannia Stadium.
He added: "Peter Crouch will always make things difficult and he has all the way through his career.
"I read the papers. There is nothing in it. It's probably people putting two and two together and making five.
"He is a big part of what we are doing and what we're trying to do moving forward. I think you saw from his performance he was not too bothered. His future is with us."
