Former England centre-back Jonathan Woodgate was adjudged to have taken down Chung-yong Lee for the penalty, and was then given a second yellow card after his professional foul on Marvin Sordell.
Mowbray was not pleased with those decisions and believed his players should have taken something away from the game.
He said: "I thought we deserved more than that and we needed a better official to referee the game because there were some bewildering decisions out there.
"The penalty was one of them and the sending-off was certainly one of them.
"Bolton started the game well, which they always do but I thought we had a decent foothold in the game and then they got a goal through a cross which just drifted in, but that's the way our luck has been going at the minute.
"I thought we were the better team but the history books will show that we lost. They won't show that we conceded a lucky goal and then a penalty, which having seen half a dozen times was never a penalty kick, but that sums up the referee's performance."