apple diseases, apple scab, sooty blotch, flyspeck and insect problems too.
The sooty looking apples have a number of fungi growing on the wax of the apple. These fungi are called sooty blotch and fly speck, which they resemble.
These molds get started usually in the interior of the tree where the fruit are wet for a long time and slow to dry. If you spray once a month in the summer you should be able to really reduce the disease. You should also do some pruning in the top of the tree to open it up and let more light in and reduce the amount of time the fruit are wet during the summer.
The apple with the single large lesion on it is apple scab. This disease got started on the fruit soon after bloom. The fruit is so clean I suspect you spray for scab but you may have been late applying one of the post bloom sprays. Apple fruit become resistant to the disease as the become waxy about a month to 6 weeks after bloom. Controlling apple scab requires frequent sprays in the spring as the tree leafs out. The young leaves need to be protected until they are fully formed when they become resistant to the disease. Because the tree is continuously producing new leaves for the first two months weekly sprays are needed to protect the new leaves and developing fruit. Generally about a month to 6 weeks after bloom the supply of overwintering spores is depleted and if the tree is free of scab those weekly sprays for scab can be dropped but you still need to spray for insect pests and include a fungicide every few weeks to reduce sooty blotch and fly speck. http://www.canr.msu.edu/ipm/diseases/apple_scab
I have attached a picture of an apple from an abandoned orchard with scab, sooty blotch and fly speck.
The spots and rings look like San Jose Scale, but I do not see the scale. Perhaps you washed them off or they were killed by an insecticide spray.
The most effective control of San Jose Scale is a dormant or delayed dormant oil application which will suffocate the scale.
These dormant sprays are applied very early in the spring when the trees buds are swelling and the leaves are beginning to emerge.
There are several home owner guides put out by other extension services in mid west states I often send people to Purdue. They have a nice color PDF that you can download and study.