Thank you for the question.  Without a photo, it's hard to say exactly what is causing the brown spots.  It might be apple maggot.  Apple maggot is an important pest throughout our state, infecting all varieties of apples. The female apple maggot flies emerge from the soil about July 1st.  She generally feeds in nearby woods and returns to the apple to lay eggs.  There is a dimple or small spot where the egg is laid.  The egg hatches and the maggot eats the apple flesh.  Brown spots appear inside the apple as a result of the maggot eating the apple flesh. The apple drops from the tree, the maggot enters the ground to overwinter, and the whole cycle is repeated again next year.  The larvae are not inside your apples now so use the apples in whatever way you like.  This information comes from a University of Minnesota Publication on apple diseases and pests.  Please read for a thorough explanation and ways to prevent trouble next year.
  http://www.extension.umn.edu/distribution/horticulture/M1235.html

Thank you-if the apples are still on the tree with these maggot trails are they stlll OK to eat? How do I know when the maggot is gone?

The only way to know the maggot is gone is to cut open the apple.  There may be good areas that you can cut out and use for sauce, pies etc.  Another expert has suggested that the brown areas could be a condition called Bitter Pit.  I have included part of this publication from Oregon State University Extension that explains the problem well : BITTER PIT IN APPLES Bitter pit causes sunken, irregularly shaped spots on the apple skin. They vary in size, but many are about 1/4 inch (5-6 mm) in diameter. Peeling the apple discloses brown, corky pockets which are more concentrated near the skin, but some may be found deep in the apple tissue. These corky pockets have a bitter flavor, hence the name bitter pit. There are usually more spots toward the blossom end of the fruit. This is not a disease caused by a fungus, bacterium or virus. It is a physiological disorder associated with low levels of calcium in the fruit. There may be plenty of calcium in the soil and even in the leaves and bark of the tree, but there is not enough in the fruit. Bitter pit may be due, in part, to competition between shoots and fruit for calcium. Heavy dormant season pruning which increases shoot growth also increases the amount of bitter pit. Excess fertilization with nitrogen also increases bitter pit. Bitter pit usually occurs in years of light crops and not in heavy crop years. Some varieties of apples are more prone to bitter pit than others. It is sometimes apparent at harvest time, but with some varieties bitter pit may appear only after a period of storage. The problem increases in severity with longer storage.   You can click on this Extension link that shows a picture of Bitter Pit on a Honeycrip.  http://www.extension.org/pages/66262/bitter-pit-and-calcium-deficiencies-in-apple-fruit#.UjtVx9KshLc  Again, it is hard to know what your apple problem is without a photo, but perhaps this information will help you figure it out.