Ooh, now this gets interesting.
At first glance I'd say that would be two apples. Apples come in all shapes and sizes, if I were to separate the two and place next to each other, I'd count two apples even if it looked like a bite had been taken out of each.
Then I started thinking about the varieties of apples. If the large apple is, for example an Akane apple, then the small one has to be an Akane apple as well. But apple varieties have well defined characteristics, including size (I think). If the small one does not qualify as an Akane apple, then we don't have two Akane apples. But it can't be of any other variety either, given that it came from the same tree as it's 'host' apple. It can't be a new species of apple either, because I'm fairly confident you couldn't tell it apart from an Akane apple based on it's genome.
I think we might have one apple and one... non-apple.