It usually hints at something crashing and preventing the update from finishing. Can be inside or outside of BTT:
Have a look at the macOS console.app in the "Crash Reports" section. If there are any recent BetterTouchTool crashlogs, please send them to andreas@folivora.ai
The appearance of folders happens for me also.
Same thing here. Still not fixed after over 2 years?!
Same.
Same here. Could someone please fix this? I think the Sparkle folders are appearing every time I restart. (There's no crash.)
I've also just discovered the range of folders created in the Applications folder by BTT. A fix would be very welcome, thanks in advance.
In the mean time: can I simply delete the folders?
yep, just delete. AFAIK the issue is outside of BTT, happens if something interrupts the updating process.
Thanks for the swift response. 
I've seen users asking about this issue since 2022, and I finally figured out what causes it on my machine.
If you keep finding weird folders named "(A Document Being Saved By Sparkle [Number])" appearing in your Mac's Applications folder every day, don't panicāit is not malware.
The Culprit: WhatsApp Desktop (or similar auto-starting apps)
Here is exactly what is happening:
WhatsApp uses a standard open-source framework called "Sparkle" for background updates. When there is a new update, Sparkle downloads it into a temporary folder (A Document Being Saved By Sparkle...) and tries to replace the old app.
However, if you have WhatsApp set to "Open at Login" (Launch at startup), the application is constantly running in the background and the files are locked. Because the app is actively in use, Sparkle fails to overwrite it. The update aborts, but it leaves the temporary folder behind. The next day, it tries again, fails again, and creates another folder.
How to Fix It
To break this infinite failed-update loop and clean up your Mac, follow these steps:
Quit WhatsApp Completely: Close the app entirely. Make sure it's not just minimized, but fully quit (you can press Cmd + Q or check Activity Monitor to be sure).
Trash the Junk Folders: Go to your Applications folder and delete all the folders named (A Document Being Saved By Sparkle...). They are just failed update files and are 100% safe to delete. Empty your trash.
Update WhatsApp Manually: Go to the official WhatsApp website, download the latest Mac version, and drag the new .app file into your Applications folder to overwrite the old one.
Pro Tip for the Future: If you want to prevent this from happening again, you can either remove WhatsApp from your startup apps (System Settings > General > Login Items), or just remember to completely quit WhatsApp once in a while so the Sparkle framework can successfully finish its background update.
I hope this helps anyone who has been annoyed by this daily folder spawn! Let me know if this solves the issue for you too.