Apparently the space is counting all old versions of files, and so the culprits of space use are likely files that have many copies, but I can't figure out how to find such files.. Painful.
I believe versions are going to get reclaimed automatically (but probably are counted against the limit).
Deleted files, however, do not get deleted automatically
- this pretty much got me locked out of my account. The client will not connect properly when you're above your quota, and the web interface is bloody useless... doesn't show totals for folders, so it's near impossible to hunt down what's taking up space. And with the amount of files I had (because versions), it was also painfully slow. Not that the local client is much faster, when I got access again by contacting support and getting some extra gigabytes quota temporarily assigned, clicking around some of the large folders would take several minutes.
(The knowledge base articles on cleaning up versions and trash via commandline didn't work either - you literally can't clean up with the client if you're above your quota. And that you have to shut down the GUI, if running, before being able to run command line actions is... bloody stupid).
Anyway, deleted files end up in a "trash" folder you have manually empty now and then, might be your issue as well, mouser?