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Unfortunately, I have heard of this happening a few times, and it's just inexcusable. Batgirl and Batwoman have both been in the Top 25 for months now. The first issues of those books both went to third and fourth printings. Currently, they are outselling Hulk, Fantastic Four, and Captain America, just to name a few.
It IS possible that at some stores, female books don't sell as well, or DC books don't, or Marvel, or Indie, or whatever. I'm not calling them liars.
But it is BAD RETAILING not to stock a book that customers are requesting. There's no good excuse for it. And it's not being very aware of the market if you don't have shelf copies of books in the top 25. That's just 6 books or so each week. We are in that group.
Seriously, I hope they take another look. Let them know you want copies. They can reorder them. Good luck!