The former Leeds United man was withdrawn 67 minutes into the KC Stadium clash, with Stoke dominating the closing stages after his substitution.
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"He's tweaked his groin," Agnew told reporters. "He was struggling at Swansea the other night, but he got through it. It's tight and it's sore but hopefully it will be okay.
"We've had various players in that three at the back and you need to have certain qualities to play central or on the right or the left.
"We had to change it and then it caused one or two problems, particularly down the left side, so we changed it to a back four.
"Credit to the players, we work at it every week and our shape now and discipline behind the ball is really, really good.
"It does frustrate our opposition at times and we're really pleased with that. It's not just the defenders, it's your front two and it goes all the way through the team."