Yes, I'm having a similar problem with Affinity Photo 2. Most of the files I have are just practice files. I figured the history that was saved with them was the culprit (although I at no time specifically saved the history when saving the files...the history just sort of stayed with them). But when I deleted the history and then re-saved the files (about 7 files), the data that Affinity Photo 2 was using ballooned from about 9.2 GB to 14.6 GB. That was definitely going in the wrong direction and for reasons I can't begin to imagine.
I' deleted the app and re-downloaded which seems the only solution at the moment...unless someone knows of an "empty data cache" setting that I'm not aware of. But overall I think the iPad apps, in particular, are the best value in software that can be found. The interface improvements are significant and profound.