Research yields test to predict bitter pit disorder in Honeycrisp apples. A test to determine whether bitter pit -- a disorder that blindsides apple growers by showing up weeks or months after picking -- will develop in stored Honeycrisp apples was developed by a team of researchers, promising to potentially save millions of dollars annually in wasted fruit. Source 4f.
Things like this do occur because you have people messing with the very essence of the apple. Instead of being happy with the apple as it is you have people who want to build a bigger better apple. I think this is a by product of messing with the simple apples.