Referee Barry Knight finally pointed to the spot for a harsh handball against Alton Thelwell after turning down a couple of penalty appeals earlier in the game.
Gary McAllister made no mistake and the home side went onto win 3-1.
But young Alton was only two yards from the Michael Owen shot that struck his hand, leaving boss Glenn very unhappy with the decision.
“I was very disappointed in how we lost the penalty,” he said. “I’ve looked at that on the video and quite honestly, if that was intention handball, then I’m in the wrong game.
“That decision was pressurised from the crowd. There were three or four decisions before that they were baying for and unfortunately he succumbed.
“It’s about key moments in the game. At 1-1 Stephen Clemence had a great chance and then the penalty.
“It was disappointing.Willem Korsten took his goal excellently and we could have got a point but that decision took it too far for us.”
By Paul Miles at Anfield
Glenn Hoddle admitted he was ‘very disappointed’ with the penalty decision that turned Sunday’s Premiership encounter in Liverpool’s favour.