Answer: A number of things can cause misshapen fruit. If the weather is cold and rainy during blossom, incomplete pollination can cause misshapen fruit. Apple scab, a fungal disease, can also cause the fruit to be less than perfect. Feeding from the rosy apple aphid can cause fruits to have a puckered appearance.
If the foliage on the trees looks healthy, I'd guess the misshapen fruit is weather related. If the leaves have spots (beginning as olive-green and then turning brown) it's probably apple scab and early spring applications of lime-sulfur should control it. If you've been spraying with fungicide but not as often as recommended, you're not providing complete protection for your trees. Follow the label directions, spraying at recommended intervals to protect your tree.
Feeding from the rosy apple aphid will cause distorted leaves as well as misshapen fruit. To protect against this pest, use a dormant oil to smother the overwintering eggs.
There are a number of other possible causes; your best bet might be to bring a sample to a local extension office or experienced grower to make a positive ID. You don't want to spray pesticides if you don't need to, and it's best to target your spray to the actual culprit, rather than spraying an "all-purpose" spray.
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