Look at the bottom of most apple apple varieties, and you'll see the remnants of the flower that gave rise to the apple itself. This flower was trod by bugs and all sorts of nasties, and its remnants can extend up to 1/3rd of the way into the apple itself. This part of the apple cannot be cleaned adequately and have been found to carry everything from bacteria, to insects, to disturbingly large amounts of pesticides sprayed on non-organic farms. It's generally not regarded as a big health concern however...because we don't eat that part anyway.
I personally once had an earwig crawl out of the bottom of an apple...AFTER I was halfway through eating it, and AFTER I had washed it. You'll never convince me to eat that thing.
Besides, the apples endocarp (the inner skin surrounding the seeds) can be hard in many varieties, and can present a throat scratch or choking hazard. Normal people usually consider it inedible.
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