Pretty much every running shoe I've had over the years after a certain amount of mileage I develop holes in both shoes inside the heel counter. The holes develop just off centre on the outside part of my back heel (for both feet). I assume it has to be the result of being a pronating heel striker? Anyone get this too, and know what the issue is?
Do you have bunions?
Your heel could be sliding in the shoe. Try the lace lock technique/knot to tighten up the heel counter. Also, put some Engo patches or duct tape in there to preserve the shoe.
You're actually melting a hole in the liner material due to sliding friction caused by an poor fitting shoe. Save up and go to a reputable pro shop where you'll get a shoe with a better liner and fit.
Cheap shoes?
What does the back of your foot look like?
Back of my foot is normal and no bunions. This has happened in just abut every shoe i've purchased. Currenty it is happending to my Hoke Bondi 7. Actually just about to go out for a very cold run and hvae my contacts on -- which make reading difficult so apologize for ay spelling errors.
Do you use one brand of running shoe or are the shoes too big? It is weird this is happening! Personally I'd try a variety of shoes. Maybe you have a really narrow heel.
I had this same problem for years. Noticeable on most shoes, but was much worse with Asics. For a number of reasons, I switched to Brooks shoes. They fit better and I wear thin socks. I used to wear thicker socks with Asics because the fit wasn't as good. Anyway, with the Brooks shoes and thinner socks, I don't have the problem anymore.
My conclusion is that like someone already said, your fit isn't great, and your heel is moving around in your show. If all else fails, try some different socks.