The puncture-type marks are likely due to tarnished plant bug and / plum curculio. When this damage occurs early, the fruit growth can become distorted.

The important key with honeybees is to avoid spraying materials toxic to bees during bloom.   Also control flowering weeds such as dandelions that might attract bees underneath and close to the apple trees. Spray in the morning and in the evening when the bees are not active. The following is a link to a MSU bulletin about pesticides and bees that should be helpful: 

http://msue.anr.msu.edu/uploads/resources/pdfs/Minimizing_Pesticide_Risk_to_Bees_in_Fruit_Crops_(E32...