Ten-man Rovers slipped to a late 2-1 loss at the DW Stadium, but there were key moments in the game that lead to their downfall.
Rovers were 1-0 up when a Jordan Rhodes shot struck the hand of Ben Watson in the penalty area, but the officials were unmoved.
"I thought we should have had a penalty," said Bowyer post-match. "It hits the lad's hands, he's saved it. I have to be careful, we are hugely disappointed but not with the performance of our lads.
"It wasn't to be for us today, I think we were on the end of a few wrong decisions.
"All credit to the fans for the spirit that they showed and it was matched on the pitch by our boys."
Rovers are back in action after the international break with Charlton Athletic the visitors to Ewood Park on Saturday 18th October.
Tickets are on open sale priced from £15 for Adults, £10 for Seniors and £5 for Juniors. Book online today at www.onerovers.co.uk