What are the item numbers of the two listings involved? The one that was won and paid for, and the relist, please.
You should always refresh the page and double check the results after listings end (whether you're the buyer or seller). I haven't experienced it myself, but delays in seeing the final results of a listing are reported fairly often. I have a fast internet connection, so I think that's why I don't see long delays, but if you're using a mobile device or your internet connection is slow, then you have to expect delays.
eBay doesn't charge for ending auctions early, unless you cancelled a bid when you ended it, and the auction would have sold. In that case, they charge you the final value fees based on what it would have sold for. This is to discourage sellers from disappointing buyers. However, eBay will automatically waive this fee once per calendar year, so if this is what happened, you must have cancelled an auction that would have sold before now.