Mikel Obi played the entire 90 minutes of the Championship clash, but was unable to stop his team losing at home.
However, O’Neill insists the game should have been won.
Stoke most likely settle for a place in the second tier next season, after their three-game unbeaten streak was ended by Gary Rowett’s team, as they are now 11 points off the top six.
“I’m very disappointed with the result, very disappointed with the second-half performance really. We showed two sides of our character today, first half we were excellent, really good play.
“But we conceded a poor goal after three clean sheets and conceded another poor goal in the second half.
“It was a defensive error that cost us, I didn’t think we’d lose the game to be honest,” O’Neill said.