I've used Cyberduck for a while now, but this is the first time I'm trying to upload photos to my website. It stops uploading and says Quota Exceeded, but I'm only uploading 3.9 MB and my webspace allowance is 10 MB. Did anyone help you come up with a solution?
It may be you have more files uploaded which are hidden. Try View > Show Hidden Files in Cyberduck. Otherwise contact your hosting provider and let them know about the incorrect quota set.