Bowyer had seen his side finally surrender 1-0 in a quarter-final replay but was unhappy referee Kevin Friend had not seen what he believed to be a clear penalty when the ball appeared to skim the arm of Liverpool midfielder Joe Allen from Ben Marshall's header.
The ball was still on course for the Liverpool net until goalkeeper Simon Mignolet turned it on to the post.
Bowyer, who had seen his side earn the replay with a 0-0 draw at Anfield, felt Blackburn should have been awarded a spot kick, although none of his players appealed at the time.
"We are a little bit disappointed with a decision that didn't go our way in terms of a penalty," Bowyer told BT Sport 1.
"His arm's out in an unnatural position and it looks like he's diverted it."
Bowyer was surprised to see goalkeeper Simon Eastwood have a late chance after he joined a Blackburn attack for a throw-in close to the Liverpool area.
Eastwood, who had pulled off good first-half saves to deny Coutinho and Glen Johnson, turned on the ball before firing straight at Mignolet.
"'Easty' at the end. I didn't know he could do that so he might be playing up front on Saturday," Bowyer joked.
"I think it was a shock that he was able to do that. It was an unbelievable turn from him.
"Our group is an honest group, they have a right good go and to push Liverpool like that over two games and still have a chance like that in the dying seconds I have nothing but praise for them."
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