Rovers twice took the lead after falling behind early on against Brighton, but they were forced to settle for a point when Dale Stephens scored with a header just moments after Jordan Rhodes had netted from the spot for the hosts at Ewood Park.
"We just said there we can't keep saying 'we've scored three goals'. We've scored eight in the last three games and we've got three points to show for it," Bowyer told reporters.
"The manner in which we conceded the goals is not acceptable. We've kept 12 clean sheets this season and we have to get back to that quickly because we're scoring goals.
"We've got to turn these performances into results and start winning games instead of drawing games otherwise it's going to cost us."
Blackburn are currently 11th in the Championship, seven points outside the playoff spots.