That's very odd. Usually an HMO licence applies to a single dwelling. A house subdivided into 3 flats would be 3 dwellings, any of which could be an HMO.
Perhaps your subdivision isn't a proper one. Do the flats get individual council tax bills, or does the house get a single one which the individual flat owners share amicably?
I've just agreed with you. Is that a problem?
I still don't understand this concept of separate flats in a HMO. AFAIK an HMO is a single dwelling occupied by more people than are members of at most two families.
If your whole house were an HMO *just because* if you added together all the occupants of all the flats, you'd get no two families of which all occupants would be a member of one or the other of, then nearly every block of flats in the country would be an HMO. And it isn't. So I think there must be something funny about your house, causing it for some reason to be treated as a single dwelling instead of three.