Boro missed the chance to go level on points with Cardiff at the top of the Championship after twice throwing away a lead and Mowbray could not hide his disappointment.
He said: "We came to win tonight and tried to be positive. We got our noses in front twice and it's tough to take when you're in front feeling reasonably comfortable.
"I think the nature of the goals were obviously disappointing for us. I don't think they had to work too hard for any of their goals and that's the most disappointing thing for us.
"I haven't seen the penalty again but I've told (Andre Bikey) you can't hang a leg out in the box, you have to defend properly, stay on your feet and push people from goal.
"I think the timing of the penalty gave them a little break because we were in the ascendancy and disappointed not to be two goals up coming into half-time, so to come in at 1-1 was a big blow for us."