The reason that cottage cheese separates is because of the way that cottage cheese is made.
Cottage cheese is made using a process of acidifying milk, which causes the curds to separate from the whey in the cottage cheese.
Cottage cheese is high in protein and low in carbohydrates and is a fresh cheese so it separates unlike other cheeses.
After the curds of the cottage cheese are formed, they are cut into smaller pieces, rinsed and often salted which turns them into the separated cottage cheese that you buy in the stores.
Cottage cheese is very healthy for you in moderation but it can lead to stomach cramps and diarrhea if you consume too much of it.
I like to eat cottage cheese as a bedtime snack because it's so delicious but I have to watch how much of it I eat.