Before I start, sorry for not doing the template, it has nothing to do with a particular version or update, it has been an ongoing thing, I just didn’t bother to say anything until now…
I actually have a somewhat similar problem to this one: What is Brave doing with Cookies now? Very confused, not to do with Cookies and other site data but to do with APPS
TL;DR: Despite clearing data something (1 app, in my case, as Cookies and other site data is in the above Topic thread) is still remaining.
I see within:
brave://settings/clearBrowserData
Under Hosted app data
it says: 1 App (Web Store)
I have tried clearing it a bunch of times in the place I mentioned above but it doesn’t work…
I had this ongoing problem for awhile and eventually found (with help from Can I use multiple tabs with an installed app? ) and uninstalled them within:
brave://apps/
But then there is still one showing…
I THINK that when I tried making my own unofficial APP and was able to do that, (and I can’t remember which site I used, maybe Wikipedia 
) which creates a “.crwebloc” file on my desktop, but I deleted it, which I have to assume I can only do manually. But AGAIN THINK, not entirely sure if that’s when this started happening again, so…
PREVIOUSLY, I also manually deleted what was in “Brave Browser Apps” as well (and DIDN’T officially uninstall them in brave://apps/ and that was my mistake before, as previously mentioned)
But again nothing is showing up in:
brave://apps/
…so why is something STILL showing up in:
brave://settings/clearBrowserData
“Hosted app data” > “1 App (Web Store)”
Despite using brave://settings/clearBrowserData with each of the Advanced & On Exit options and restarting Brave.
p.s. I have created a test profile and it’s still happening in that too.