These apples have Apple Scab, the most common and most destructive pest affecting apples. In addition, there is a good chance these apples are affected by a second problem, "bitter pit". It is not uncommon to have problems with both in the same year.

Apple Scab can completely destroy an apple crop. Symptoms include lesions on fruit, heavily "burned" and cracked areas on fruit, as well as discolored and distorted leaves.   Below is an excellent UC Davis site that gives very complete information about the pest and its treatment.

When you have only one or two trees, the first line of defense is to completely rake up all fallen leaves. The fungus was formerly believed to overwinter on the tree trunk and branches, and this was the primary reason that dormant spray for apples was always emphasized. It is now known that it does NOT overwinter on the tree--it overwinters on fallen leaves, and is spread back up into the tree from those leaves in our moist spring weather. Raking up all of the fallen leaves may control the problem down to tolerable levels for homeowners..

When a small home orchard has too many trees to make raking feasible, an inferior alternative is to spread urea fertilizer, or some other fast-release high-nitrogen fertilizer in winter after full leaf-fall, as the fertilizer will aid in the quick decomposition of the leaves. (Unfortunately slow release fertilizers, like the common organics made of feathermeal or cottonseed meal, etc., will not work for this purpose--they release the necessary nitrogen too slowly.)

Chemical controls can be substantially more effective. As the UC Davis site explains: "Fungicide sprays are necessary only if the weather is rainy and leaves are likely to remain wet for 9 or more hours. Fungicide applications require careful attention to timing, as preventing early infection is the most important step toward successfully controlling later fruit infections. It is difficult to prevent secondary fruit infections once primary infections occur." Unfortunately, here in the Willamette Valley, these conditions are guaranteed to occur every single year,  So the most common strategy for most home growers who actually need to get a healthy crop is to use approved chemical controls at least once early in the spring--soon after the buds begin to break--combined with meticulous removal of all fallen leaves, all year long. (Obviously, do not recycle the fallen leaves in your home compost. Send them away in your weekly compost pickup!)

As is often the case, some varieties are more susceptible than others.  See the table in the link below for common varieties that are very susceptible, or more resistant.  But be aware that because disease conditions in our area are so excellent, even so called "resistant" varieties commonly get apple scab here.

More specifics on Apple Scab, see this link:http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7413.html

The apples in your photo probably also have a completely different problem as well. Commonly called "bitter pit", this is not a disease or a pest, but a physiological condition brought on by a lack of calcium. There is generally NOT a calcium deficiency in our soils, however. The problem is low or irregular soil moisture around the tree, which hinders the tree's ability to distribute the available calcium up to the fruit.  The result is fruit that tastes "corky" and stores badly.  The most visible symptom before the fruit is picked is the presence of small indents or dimples around the surface of the fruit, and these are not pronounced in your photo. But bitter pit frequently also causes interior discoloration, including streaking, through the body of the fruit, much as your photos show. And unless the grower has been very conscientious about monitoring soil moisture and irrigating regularly this year, with our unusually dry spring, then rain, then a summer that has been even drier than usual, bitter pit is going to be even more common this year than usual. (Other conditions that increase the incidence or severity of bitter pit include heavy pruning during the dormant season, over-thinning of apples, and too much nitrogen fertilizer.)

Varieties that are particularly susceptible include:  Honeycrisp, Northern Spy, Gravenstein, Grimes Golden, and Baldwin.Golden Delicious is less susceptible.  More resistant are Delicious, Gala, and Winesap.