Nikola Zigic's late strike condemned Boro to a third successive defeat and their sixth in eight matches.
Boro's poor form has seen them slip five points off the play-off places, and Mowbray conceded: "We are making it difficult for ourselves.
"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."
Zigic avoided picking up a second yellow card for what looked a deliberate handball, but Mowbray added: "Listen, I'm not going to moan about what the ref did or should have done.
"There were plenty of things we should have done in the build-up to prevent that goal."