I’ve run into this condition three separate times in grocery apples. I’ve quit buying honeycrisp last year because it got so bad. As I’ve started to grow my own apples I’ve wanted to specifically avoid this problem. Thing is, I don’t know what it is. I pulled this photo off the internet as representative of what I’ve seen, and that photo was from a Reddit group where they confidently proclaimed it as blossom end rot. That typically rots to the skin, though, so I don’t think that’s it. It looks more like bitter pit, but giant and not visible at the surface.
Every time I’ve found this it’s like a ball of mold in the middle of the apple, slightly off the core. It’s never visible from the surface. It smells strongly of mildew.
This was in Honeycrisp, btw. I’m not familiar with how it rots, so maybe it’s common in that too? I had never seen it before last year, then all of the sudden it was rampant. Probably 3 out of 12 apples had this. I’m presuming they came from the same grower since they were in near succession, but I’d have no way of knowing for sure.
I have seen this in some apples over the years and have no idea what it is called. It would be interesting to find out exactly what it is and what causes it. To me it looks almost like a tumor or cyst of some kind, if it were put in human terms.