Rovers have not won since they beat Arsenal in the FA Cup in February and with Huddersfield drawing with Peterborough, the Lancastrians dropped into the relegation zone.
The visitors took the lead early on when Chris Kirkland brought down David Dunn, with Jordan Rhodes scoring the resulting penalty before Jermaine Johnson equalised.
Leroy Lita converted a penalty after Josh Morris was adjudged to have fouled Reda Johnson and although Scott Dann levelled Johnson was hand again to snatch a winner.
Bowyer felt his side deserved more out of the game and was disappointed with the officials' role in both penalties.
"One or two of the decisions haven't gone our way," he said.
"Ours was a definite penalty, the goalie pulls him back and gets a yellow card - he's going to score, so these are the things that are sent to test you.
"(For their penalty) their lad's a big 6ft 5 lad and he goes down like he has been hit by a truck. No disrespect to our lad, but our left-back Josh Morris isn't built like a truck. The linesman possibly crumbled under the pressure a bit. These are the things that change games.
"We aren't going to feel sorry for ourselves; it's in our hands still we have a game in hand.
"Of course it's difficult, it's a difficult situation, but I'm not going to shirk, I'm going to give it my best shot, we can only fight. The players care, they really care.
"Our games are winnable games. We can get 18 (more points) but our luck has to change.
"Matters off the field don't help, but they are out of our control."