Boro missed some good chances and were caught cold by a late Birmingham strike from Nikola Zigic as they lost 1-0 at the Riverside.
It was a third successive defeat and sixth in eight matches in the npower Championship and, although they remain ninth in the table, Boro are now five points adrift of the top six with just eight games left.
"We are making it difficult for ourselves," said Mowbray. "We understand we need to win games to give ourselves a chance and that now we have one less game to do that.
"But it was a fine margin game. It could have gone either way but unfortunately it is another one that fell the wrong side of the line for us.
"We asked questions of them and had our chances to score but we never took them.We have maybe missed a few chances to kill games off in recent weeks but that is where we are as a team."
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