The Brewers were on track to leave the Toughsheet Stadium with a share of the spoils after Jack Armer cancelled out Sam Dalby’s opener.
But Dalby struck again in stoppage time to leave the Brewers just above the relegation zone, with one win in six in the league.
“I think both goals are really, really poor goals,” Bowyer told the club. “We came here with a gameplan, against a really good team, well coached, great movement, good players. Look at the changes they are making as well.
“We gave a really good account of ourselves, we had some wonderful moments, first half especially.
“I just questioned the players’ desire to get on the end of it, to want to go and hurt themselves, push themselves beyond.
“We come in all square and the crowd were getting agitated as they do here. The first goal is a really poor goal from us on three separate incidents in the build-up to it.
“We get a goal back and I am delighted for Jack, brilliant for him. Then we are pushing and you can feel it. It is just those key moments, really disappointed with the manner of the goal.”
Burton had some good moments in the first half but ultimately failed to make them count, with JJ McKiernan and Kain Adom both going close.
“We didn’t work their goalkeeper enough,” Bowyer insisted. “Second half, we hit the inside of the post with JJ, who I thought did ever so well for an hour on his return.
“Delighted to see Seb (Revan) and Alex (Hartridge) back on the pitch, and Tyrese (Shade) coming back into it. I have got options now because we have to eradicate what has been going on.”
He added: “You have got to hit the target, you have got to do your job properly. We have a set play late on and hit the first man.
“We don’t track a runner for the second goal, we don’t follow in on both. They are the basics that you have to do.”