Well, half the stuff you get at CM is the same stuff you can get at HEB, except everything is marked up. The typical thing you can say is that they can get away with it and it makes them more money. And heck, that CM is often crowded as well. The only thing they really have over HEB would be meats and cheese. Most of the produce in the store bear the same labels as their HEB counterparts, and the other half are really expensive produce that your wouldn't buy anyway.
But I was also wondering if maybe they weren't just money-hungry people who are legitimately trying to run a business that's fair to them and their customers. I know that there are some pretty expensive specialty items in the store that no one is going to touch and will probably have to be thrown out at some point, particularly in the produce department. Are those the bargain items that have to be sold at a lower cost and made up for by other costs? Kind of like eating fancy stuff in a restaurant; your halibut is going to have a lower markup than the chicken pasta dish.