iCloud storage doesn't add up
This might be a little late but I had the same problem. Went to the genius bar and they said to call Apple Care. I called Apple Care three times. The first two people said that there are other item which could be taking up space and couldn't provide a solution. The third one was more experienced and fixed the problem within minutes. She had access to the "iCloud support tools". This is a tool the Apple iCloud team has access to (but we as consumers don't). She used the iCloud storage repair kit and within minutes, my devices refreshed and the free space showed up. Apparently this problem occurs when you upload a file, it gets corrupted, then once deleted, iCloud doesn't recognise the space as being free. Hope this helps.