Apples can have what is called "bitter pit" and it seems Honeycrisp are sensitive, but other apples get it also. Briefly, there is a calcium deficiency, so steps to treat it take some time. Here are photos from the OSU plant pathology clinic to compare with your fruit. Sometimes the apples still taste okay.
This prior Q&A gives a good answer and includes links to the research and steps to take. There is also this Q&A about using the apples for cider. The explanation about bitter pit is phrased a bit differently. I like to read multiple explanations because I sometimes understand one expert more easily than another.
I hope your apples improve each year with treatment.