David Nugent scored the penalty that followed to make it 2-0 going into the break following Lloyd Dyer's opener but Bowyer, who saw Jordan Rhodes half the deficit from the spot in the 70th minute, thinks it should never have been awarded in the first place.
"I think you always judge it by the reaction of both sets of players," Bowyer said.
"I think you could see what our lads thought of it. And I think if you look on the video again there's only one Leicester player that really appeals and even then it's half-hearted."
He added: "I thought we didn't defend very well for the first goal and then we were just preparing to go in at half-time and just started to come into the game and got into one or two good areas against a very strong and experienced Championship side, and then the linesman gives a decision that changes the course of the game."