The successful penalty from Antoni Sarcevic and an 83rd-minute header from skipper Mark Roberts, either side of Scott Hogan's leveller for Dale, proved enough to earn the three points for the visitors.
"It wasn't a penalty and it's not a question of whether the referee has made an honest decision because honesty doesn't pay dividends for me," cried Hill.
"We've watched it again and again and again and it's not a penalty. It's a poor decision which, to a large degree, has affected the outcome of the game.
"It was a difficult day with respect to the conditions - the wind spoils any hopes of a spectacle. But I am concerned by the defeat and the ramifications of losing for the players. I'm not sure we deserved to win the game, but we didn't deserve to lose it."
After a chanceless opening 20 minutes, Fleetwood edged ahead when referee Clark awarded a spot-kick for a foul on Charles Taylor by Rhys Bennett.
Sarcevic fired home a hard, low drive from the penalty spot, beating Josh Lillis despite the goalkeeper guessing the right way.
The home side were level in the 40th minute, though, as Ian Henderson's corner from the left was headed goalward by Ashley Eastham and Hogan reacted sharply, flicking the ball into the net from close range.
Nathan Tyson wasted a good opportunity just before the break when, unmarked at the back post, he headed Taylor's cross high and wide.
Fleetwood went even closer in the 48th minute when Gareth Evans found Sarcevic at the back post with just Lillis to beat, but he drilled a first-time effort against the upright and Dale were off the hook.
But when Junior Brown's free-kick seven minutes from time was headed against the post by Nathan Pond, Roberts was there to capitalise, stooping low to head the ball across the line.
- Sports & Recreation
- Antoni Sarcevic