Napoleon's original argument against the windmill is that building it will take up too much time and cause the animals to neglect the farming and harvest. In reality, the windmill would make the farming much easier, but Napoleon is forced to argue against it to depose Snowball. Once Snowball is out of the way, Napoleon puts the windmill construction into motion, but without Snowball's expert delegation skills, the animals are forced into working harder for fewer gains.
The needs of the windmill must override everything else, he said. He was therefore making arrangements to sell a stack of hay and part of the current year's wheat crop, and later on, if more money were needed, it would have to be made up by the sale of eggs...
(Orwell, Animal Farm, msxnet.org)
Because he tries to accomplish everything without proper planning, Napoleon finds that the farm is unable to survive without selling part of the harvest; this nullifies the total gains from the windmill project, causing the animals to go on short rations. Although Snowball's plan also required sacrifice, it would have been accomplished slower and with more planning for emergencies. Napoleon's focus on the windmill leaves the farm unready to cope when their hard work falls apart (the walls are too thin, an issue that Snowball would have calculated earlier). The following winter is hard, with little food, and the result is that Napoleon continues to increase his power through force.