It was the Lions' second defeat in their last four matches - a run that has seen them slip out of the Championship play-off places.
Jackett said: "Looking at the key points in the game we've missed a penalty, the sending off (of Adam Smith) was a harsh one which we will be appealing, and the winning goal looked close to being offside.
"When we went down to 10 men, it looked like there was only going to be one winner. Going down to 10 galvanised us and we played better so it's hugely disappointing to lose.
"We were going all out for the win and it showed at the end. The penalty miss wasn't the only turning point in the game but it did have an effect on its outcome.
"I don't think we did enough when we had 11 men to win it. The character we showed when we went down to 10 was admirable, but the red card looked harsh and is baffling to me."