Knowing how good the Hornets are at counter-attacking, the manager had tried to ensure they weren't allowed to play the game on their terms.
The plan worked well for most of the opening half but was derailed by an uncharacteristic error from skipper Rhys Williams, who chested the ball back well short of keeper Jason Steele, enabling Matej Vydra to nip in and score.
"I think we beat ourselves today," said the manager. "We had all the chances but didn't score and then we shot ourselves in the foot with the goal we conceded.
"We really smothered them in the first half and I thought we were on top but to go 1-0 down in the manner we did was very disappointing.
"We had a full week to prepare for it and I thought the gameplan was good but we needed to score the first goal.
"We showed we're a decent side and why were near the top of the table. Yet we've come away with nothing against the team with the best goalscoring record away from home in the division.
"It's frustrating because we played so well for an hour, but that's football."
Once Gianfranco Zola's men got their noses in front they made it hard for Boro to get back into the game, posing a potent threat at the other end of the field.
"They are as good a team as any in the league at counter-attacking," said Mowbray. "They scored two and could have had four or five on the break because they're very good at it.
"Steeley had to make some good saves in the second half because they're exceptionally good when you give them space, which they didn't have in the first half.
"Our defenders had almost nothing to do in the first half but being a top player is about keeping your concentration.
"As I've said to the players, if they're going to get to the next league up, if you go a goal behind you're going to be in trouble against good players who make good decisions.
"I used to play football through fear of not making a mistake. Rhys has been out for four months and has only been back for four games. He has to get back into the swing of things."
Boro have little time to lick their wounds and face a massive game on Friday night against the team who overtook them in the npower Championship table today, Leicester City.
"The frustration is we could have gone second with a victory today," said Mowbray. "But we have to put it behind us and move on.
"Any team that wants to stay at the top need to react by winning football matches and we're looking forward to Friday's televised game at Leicester.
"Leicester are a good side with good players. They have a fabulous goalscoring record at home and it's a challenge we have to try to rise to."