Does a seed rot with apple?

Yes, a seed will rot with an apple.

An apple is a fruit that contains a high amount of water and sugar. When a seed is placed in an environment that is high in moisture and sugar, it will begin to germinate. The seed will absorb the water and sugar from the apple and begin to grow. However, the apple will also contain bacteria and other microorganisms that can cause the seed to rot. The seed will eventually rot and die if it is not removed from the apple.