What happened to the milk that disappeared and to the apples from the orchard?

The milk and apples go the pigs. The pigs commandeer all the milk for themselves, even though the hens mentioned that Farmer Jones used to mix some of the milk in their mash. Of course, the animals don't know for certain at first that the milk has gone to the pigs. The scene unfolds as follows:

"What is going to happen to all that milk?" said someone.
. . .
"Never mind the milk, comrades!" cried Napoleon, placing himself in front of the buckets. "That will be attended to. The harvest is more important. Comrade Snowball will lead the way. I shall follow in a few minutes. Forward, comrades! The hay is waiting."
So the animals trooped down to the hayfield to begin the harvest, and when they came back in the evening it was noticed that the milk had disappeared.

The pigs are unanimous in saying they need all the windfall apples for themselves. They explain to the other animals that they need the apples for their brainwork. They say they are eating the apples for the sake of the other animals, though its hard to imagine that that is the real reason. Note, too, how in the quote below, the pigs admit to drinking the milk:

The whole management and organisation of this farm depend on us. Day and night we are watching over your welfare. It is for YOUR sake that we drink that milk and eat those apples.

This shows how, from early on, the pigs are setting themselves apart from the other animals and treating themselves as a privileged class. The other animals at first expect the milk and apples to be divided up evenly, according to the principles of animalism, and are too quick to believe the lame explanations the pigs come up with for taking the extra food.