Darius Henderson scored a last-minute winner at Ewood Park to condemn Rovers to their first league defeat of the season.
"That is two games now in succession in the league where I don't feel we got what we deserved," he told Radio Rovers.
"Don't get me wrong it wasn't a classic that is for sure, and we know that we can play a lot better than that like we showed last week at Derby.
"I thought there were some fighting qualities and some determination but we've just got done at the last minute and it is a cruel blow."
Despite the defeat, Bowyer feels that that there has been many positives to take from the season's opening fixtures and that there is more to come from his side.
"I've just said to the players that Nottingham Forest are going to be there or thereabout so it is credit to us in how far we have come so quickly," he said.
"I think there are a lot of positives we can take from it but we are absolutely gutted because in the two games we feel we should have deserved more from them."
Blackburn travel to Doncaster Rovers in their next Championship fixture on August 16.