Rovers had the better of the game throughout, creating a dozen decent chances, but slack play at the back and inspired saves from Tomasz Kuszczak proved costly.
"We can't keep giving teams goals then getting plaudits for how well we've played and how we were the better team," said Bowyer. "We can't keep doing that.
"They were three poor goals, we can't keep giving the opposition goals, we can't keep giving teams a head start.
"We have to cut out the individual errors, we've not been carved open today.
"For me their man-of-the-match was their goalkeeper. That tells me we were well in the game but we've not been ruthless enough.
"We've just got to get ourselves back ready for the Reading game."