The daycare man should only say that if the two Pokemon can't breed with each other, either because they are from different egg groups, or because they are the same gender. However, your situation is strange because Ditto and Hitmontop should always be able to breed. He should be saying "the two don't seem to like each other" (assuming both have the same trainer ID number). Make sure you haven't mistaken what he is saying, as that is the only thing I can think of.
Source: Bulbapedia
