Mowbray had seen his side claw back to level an early Albert Adomah opener when Ishmael Miller stabbed home from a corner.
Then at 1-1 Grant Leadbitter's corner was spilt by City goalkeeper Tom Heaton and seemed to go over the line before being hooked clear - and the decision was 'no goal'.
To make matters worse, City scored two more on the counter thanks to late strikes from Stephen Pearson and substitute Steven Davies.
But Mowbray refused to point the finger at the pivotal 'ghost' goal.
"There's no mileage in blaming the referee over things like that," he said. "We've had a few things like that go against us this season but also a few go for us.
"You may wonder if the fog may have been a factor in him or the assistants not seeing it but if the referee doesn't give it, there's no point moaning. It won't change the record books.
"The result was disappointing and frustrating but that is down to the way we performed, and it must be said, the way Bristol performed. They played well on the counter.
"Things just didn't go to plan. We went more direct and it didn't pan out. We changed the shape for the right reasons but it didn't come off.
"But you can't over-analyse it. We are still in the top six and there are still plenty of games to play. Luckily we have another one here on Tuesday night against Huddersfield, so we can put it right quickly."