Visiting goalkeeper Asmir Begovic twice denied Hull in the first half, making smart stops from Ahmed Elmohamady and Yannick Sagbo.
Egyptian Elmohamady went close again after the break, but Stoke gradually grew into the game, and Allan McGregor saved twice from Peter Crouch to rescue a draw for the hosts.
Ryan Shawcross also hit the crossbar as Hull clung on, and Agnew was at a loss to explain their failures after the interval.
"It wasn't a classic," he said. "I think everyone seems to remember the second half when Allan McGregor's made two terrific saves, but so did their goalkeeper.
"First 45 minutes, I thought we dominated the game, we were the team pressing forward, so we were pleased going into half-time.
"Second half was the complete opposite. We were a bit loose with the ball, we didn't move up the pitch with the ball as well as we can so consequently Stoke gained a little bit of momentum and with players like Peter Crouch they're always going to create chances when crosses come in.
"We just lost a little bit of the momentum for whatever reason second half, but the pitch was a little bit lively and the wind was swirling so it's not easy for all the players."
Hull now have the best home defensive record in the Premier League, having conceded just three goals in eight games at the KC Stadium.
While Agnew is delighted with their performances at the back, he now wants them to move on and improve going forward.
He added: "They work at it and they get their rewards from putting the work and the effort in to that defensive record.
"It's pleasing and it's rewarding and I just think our ball retention and moving up the pitch and our attacking play can get better and we'll continue to work with that."
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