Instructions
Open the "Options" menu and disable "Puppy Vision." This will allow you to interact with the game's environment outside the perspective of the characters.
Enter De Vil Manor, the large mansion you see as soon as the game world loads. Scattered inside this location you will find most of the existing 99 puppies; others are in a nearby shed, and the last two are hiding under Cruella De Vil's car.
Choose the hand-shaped "Select" tool from the "Tools" menu on the left of the screen.
Use the arrow keys to navigate through De Vil Manor until you find a puppy you want to delete.
Left-click the puppy that you want to delete and press the "Delete" button on your keyboard. Press "Yes" on the menu that pops up to confirm your decision to delete the puppy.