IME most hotels verify your rate at check in, either verbally (not very common), on a form you sign, or on your key card. Ideally, this is the time to discuss any rate discrepancies.

If the hotel didn't inform you ever (I started to write "until after you left" but then realized that you learned about the new rate when you saw the credit card bill), IMO it's wrong. OTOH they could have told you (hopefully before arrival) that you no longer had a reservation.

Check your confirmation carefully to see whether there's any statement about when the deposit will be taken or anything about expired cards. I consider it unreasonable for hotels to charge nonrefundable deposits at random times, but some seem to operate this way. Some hotels also notify people of problems with the credit card attached to a reservation as they're traveling to the hotel and give them almost no time to resolve the problem before canceling the reservation.

BTW, do you know whether the hotel was full when you stayed? If you were eligible for a cheaper rate, the hotel should have never tried to give you the full rack rate. You might want to play with the website to see how much cheaper the nonrefundable advanced purchase rate tends to be on some random nights.

You might want to call your credit card company and discuss whether they consider this practice to be OK. Implicitly, you're asking about what would happen if you were to file a dispute, but I wouldn't use this word then. You want to know how the hotel should handle the situation, in their opinion, and what you should/can do.