Matt Smith had put the visitors ahead but Doncaster dominated after the interval and looked to have grabbed a deserved leveller when Theo Robinson fired home in the 66th minute.
The linesman kept his flag down when Robinson latched on to Ritchie Wellens' through ball but raised it moments later when the striker's shot hit the back of the net. Leeds then went on to win 3-0.
Dickov said: "I haven't had an opportunity to speak to the referee yet but intend seeking him out for an explanation.
"I've had the benefit of replaying the incident about 20 times on the video and Theo is clearly a yard on side.
"But the late flag has baffled me as much as anything else. It looked as if the linesman thought he was on side but changed his mind when Theo scored.
"It's a massive decision because we were all over them at that stage and had we got a goal it could have changed the course of the game.
"We've gone on to concede a couple of poor goals from our point of view but I can't be too hard on the players because we had by far the better of it against a very good team.
"The first half was scrappy and you have to give them credit for taking their chances when they came.
"You can't afford to give players of that quality the opportunities we did but other than that I was quite pleased with the performance despite the result."
Smith headed home a free kick from Alex Mowatt in the 20th minute but Rovers were on top throughout the second half until Ross McCormack added the second in fine style in the 76th minute and Rodolph Austin grabbed the third in the closing stages.
Leeds manager Brian McDermott admitted he was a relieved man after the final whistle.
He said: " It was a tough game - there's no getting away from that.
" I thought we were good value for the lead in the first half but we just couldn't get out of our half after the interval.
"Doncaster came out in the second half and played really well. We had to change our system to combat that and we did better when Michael Brown came on midway through the second half.
"I'm happy to come away with three points and a clean sheet because they put us under the cosh for a good 20 to 25 minutes.
"But you have to find a way to win in these situations and it helps when you have a player like Ross McCormack who can't stop scoring and took his goal really well.
"That gave us some breathing space and I always thought we would see the game out after that."