Rovers went into the match looking to bounce back after losses to Bolton and Burnley, but they turned in a below-par display that was settled by Lewis Grabban’s goal midway through the second half.
"We knew today was going to be a difficult game because of the emotion of Sunday," Bowyer told Radio Rovers.
"But It was flat all around the ground and it was flat on the pitch.
"Understandably, Sunday was a big game, but we started off okay in the first five, ten minutes which was pleasing, but we've not really made their goalkeeper work enough tonight.
"For long periods I thought it was going to be a 0-0 game but the lad has pulled a shot out from nowhere, again we should have defended it better.
"Overall it was too flat from us tonight. It is our job to pick them up now and get them ready for Saturday against Huddersfield and come out fighting."
Tickets for Saturday's match away at Huddersfield Town are currently on open sale, priced at £25 Adults, £15 Seniors, £10 Under-18s and £5 for Under 8s.