In Chapter 6 of Animal Farm, there is a storm in November and this is what destroys the windmill. Napoleon had initially opposed building the windmill, but after he chased Snowball off the farm, he began supporting the windmill. In fact, he made the windmill the animals' top priority, even to the point where other duties became neglected. As those duties were neglected, Napoleon began trading with other (human) farmers for needed supplies.
Since Napoleon had put so much support behind the windmill, he feared looking like a fool. So, instead of taking responsibility or even simply blaming the weather, he blamed Snowball for the windmill's destruction.
Do you know the enemy who has come in the night and overthrown our windmill? SNOWBALL!" he suddenly roared in a voice of thunder. "Snowball has done this thing! In sheer malignity, thinking to set back our plans and avenge himself for his ignominious expulsion, this traitor has crept here under cover of night and destroyed our work of nearly a year.
Napoleon blamed Snowball, rather than the actual cause (storm), because he felt it would further demonize Snowball in the animals' eyes. In turn, Napoleon also hoped this would reestablish the animals' loyalty in himself as their trustworthy leader.