Yes, I checked in files to later on remove them (delete/private) and then checked in again. However, this didn't reflect in lower cloud storage.
However, I'm in the beginning of my project and most have been testing technical solutions. Because of this I just decided to remove the repository completely and reupload it in a new one. I went from 5.7 GB to about 2.5 GB. But because of Plastic SCM security feature my old repository are still in the cloud storage but should be deleted with a couple of days.
So I guess my issue is fixed now.