Goldeen can learn Waterfall naturally, right? But Waterfall is also an HM move. So, if Goldeen learned it naturally, and you wanted to delete the move, would you have to go to a Move Deleter or not?
If the move is an HM move in that game, then you have to go to the Move Deleter regardless of how the Pokémon learned the move. If the move is not an HM move in that game then you can forget it normally.