A: I suspect the problem is poor pollination. Cut the apple in quarters and you will probably find the small half has fewer seeds, perhaps none at all, while the larger one will have more seeds.
As a rule, the more seeds that form inside a fruit the larger the fruit will be. Small seeded varieties like kiwifruit and feijoas need good pollination to produce large fruit. Lack of bees, cold or windy weather, or lack of a pollinator variety at flowering could cause your misshapen fruit