After a goalless first half, Rovers were no match for the promotion-chasing Hornets who scored four unanswered second half strikes.
"At half time we were well in it but the first goal was crucial," said Bowyer after the game.
"In the first half we felt that we hadn't played as well as we are capable of and if we upped it then we'd have a chance of winning the game.
"But everybody in the dressing room is disappointed with how we went about it. It isn't us, we haven't been like that in the last couple of weeks.
"We wanted to make a change but the referee wouldn't let us and they went and scored the second goal.
"Then we just needed to make sure that we stayed in the game, the players are disappointed, they are not happy with the way they responded to going behind.
"We now have to put that to bed as quickly as we can, regroup and go again on Tuesday."