The "brown stuff" in your apples is likely caused by codling moth. In small orchards, sanitation by removing and disposing of young damaged fruit can be helpful in reducing codling moth. Check regularly throughout the season for fruit with frass-filled holes. Removing and destroying infected fruit prior to larvae emergence preceding pupation can help reduce overall populations. Picking up dropped fruit from the ground likewise can be an effective sanitation measure.
The traditional control program is to spray trees with insecticide. Apply a first cover spray about 10 days after full petal fall (all petals are off) or 17 to 21 days after full bloom. Insecticides must be timed to target newly hatched larvae before they bore into the fruit. Multiple sprays are often necessary with applications up to every 10-14 days; however sprays can be reduced by monitoring for adult moths with monitoring traps to properly time insecticide applications to the hatching larvae during the growing season.
But if you prefer to use greener methods, the following can reduce codling moth damage.
Homeowners can bag individual fruit (clusters thinned to one fruit) in paper bags approximately six weeks after bloom, however this can be labor-intensive and more challenging for cultivars with short stems. Fruit will mature completely within bags, however color development on red varieties may be affected.
Pheromone lures and traps. Pheromone traps are made by attaching pheromones to a sticky bottom trap. Male moths are attracted to the scent and get stuck to the board. The traps monitor moth flight and indicate when you need to spray; only when it is necessary and most effective. If there are no other hosts (apples, pears, plums or walnuts) in the area, sometimes a large number of traps can attract and kill most of the males, significantly reducing breeding.
Sanitation and banding. Sanitation is the most important practice that is environmentally safe (or safer). If you remove and dispose of damaged young fruit throughout the season, you can help reduce future generations. Larvae continue to feed inside the fruit after it falls from the tree. Remove fruit promptly.
Installing bands covered with Tanglefoot ™ (available from garden supply stores) around the trunk of your fruit trees, 18-24 inches from the ground, can also reduce populations. Mature larvae move down the tree in search of a place to pupate and can be trapped in the sticky substance. While this method reduces the population, it does not provide complete control because many larvae overwinter on the ground.
Here are some publications to check out:

https://pnwhandbooks.org/insect/tree-fruit/apple/apple-codling-moth

https://extension.oregonstate.edu/news/how-safely-control-codling-moths-home-orchards

Hope this helps!