While I do not want to name names, I have worked for a very large retailer that everyone in the US would know that stored credit card information for quite a long time. They are large enough to do large chunks of their credit card processing themselves, instead of having a third party processor. They even have their own set of cards that they process themselves. It might have changed in the last few years though.

Either way, they did take PCI DSS seriously, and passed audits: dual control requirements for keys and all that. Still, accounting could print reports with many credit card numbers, although it was all logged and relatively well tracked.

I have not worked in a lot of big retailers though, but I have seen others that featured searching for a missing receipt by credit cards number, or refunds to the original CC way past the window where a processor can just reverse a charge. There's also online retailers, that definitely remember your credit card number. So I suspect there are plenty of retailers that at least have historically kept CC numbers, whether being PCI compliant or not is another matter entirely.