Speaking to the Press Association, Mowbray, who took over the Boro hot-seat from former City manager Gordon Strachan, said: "We missed a penalty and they scored a penalty.
"I thought we controlled the game reasonably well after the first 20 minutes where they had a number of free-kick and crosses into the box.
"We didn't really feel threatened, particularly in the second half.
"We are very disappointed to lose a game we didn't think we should have done but there you go, that's football, you have to look at the positives.
"If you're a penalty taker and you miss, you get asked questions but if you put it in the bottom corner no one says anything.
"If our performance levels stay like that we will be fine but you need to find the formula to win games.
"Marvin Emnes hit the crossbar when he only needed to side foot it from inside the six-yard box and it is those fine margins which are the difference between winning and losing football matches."