Corry Evans gave Rovers the lead early in the first half before James McClean equalised for the Latics in the second half.
Shortly before scoring the winner McClean was lucky to stay on the pitch after a bad tackle, a fact that Bowyer was quick to point out.
"We score an outstanding goal and then we've had two cleared off the line - one unbelievably so," said the Rovers boss.
"Their goalscorer shouldn't have been on the pitch, it is as simple as that for the challenge Markus Olsson. So we are disappointed with that.
"I think it was a typical local derby, the game was scrappy, the pitch wasn't great and both sides went hell for leather for it.
"On reflection we should have won the game with our chances. We are disappointed that we didn't take all three."
The result sees Blackburn remain in tenth place, eight points off the last playoff place.
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