Usually with questions we use "any." "Is there any milk in the box?" You could answer, "There is some."

Because it is NOT a yes/no question. He is actually asking the question because he has some interest in the milk. He probably wants to drink some. Is there any milk? = Neutral yes/no question. Is there some milk? = Question where there is some interest in the actual milk. Got that?

"Milk" is a non-countable noun. If you wish to quantify, you must say "a bottle" or some such.