The most likely explanation is both mundane and eminently explicable: It could just have to do with Costco’s supplier. See, Honeycrisp apples are a very recent cultivar that was only released to the public in 1992 after being designed at the University of Minnesota. Because of where they came from, Honeycrisps were designed to be grown in colder temperatures. However, thanks to their explosive popularity in recent years, farmers try to grow Honeycrisps in various climates for which they weren’t designed. It’s inevitable that this would affect their quality.
There’s also concerns related to their color which can allegedly result in apples that aren’t as ripe as they should be. By design, Honeycrisps start to get red when they’re at peak ripeness. The problem is certain cultivators are theorized to have messed with Honeycrisp genetics to make them turn red faster — meaning they wouldn’t actually be ripe any earlier, but would look like they were ready for store shelves, and thus increase the turnaround time on the crop itself. Through no fault of its own, if Costco sourced from a supplier doing this, the apples wouldn’t be ideal.
So are the Honeycrisp apples at Costco not up to par? It’s hard to say … but some customers certainly aren’t happy.