Does the bucket have versioning enabled? You should be able to see it in the bucket properties: Versioning: enabled. If so, when you are looking at the empty folder, at the top there is a switch "show versions", switch it on. Do you see some objects with hashes?
Try to delete them. Be careful, there are versions and "delete markers", you have to delete both in order to completely empty the bucket.
Another option: you are billed for requests and data transfers https://aws.amazon.com/s3/pricing/?nc=sn&loc=4
If something is checking the bucket rapidly, it can generate some costs.
But most often the delete versions is the reason.