Apples rotting

If you've been having a lot of rain and cool weather, then yes, it's the weather affecting your apples. They can take only so much moisture before they 'overdose' and begin rotting. Cool weather only makes it happen faster. If it was cool and dry, you'd likely get a harvest.
You see something similar in toms if they get too much rain, but mostly splitting with them before pests move in.

As for protection, it's already too late so just keep cleaning up the rotting ones so no pests or diseases overwinter in them.

Thin the remaining apples to make sure that you have individual apples with plenty of air movement all around them.  You could remove a few leaves around the apples to help this as well.