You don't specify and it's highly dependent but in most cases when an app is misbehaving it's an issue with preferences. You can reset most apps with `defaults` without blowing away all its data. There are some intricacies with how macOS handles preferences, so you should avoid manually editing related .plist.
The case where I want it to auto clean up is where it is repeatedly broken and I never really got to using and configuring it yet. It's pretty rare.
Of course, `man defaults`. You can modify the preferences and potentially fix it, backup preferences, etc. Again I must stress that you use `defaults`, the .plist on disk isn't always accurate even if you terminate the app and reboot the machine.
> The case where I want it to auto clean up is where it is repeatedly broken and I never really got to using and configuring it yet. It's pretty rare.
There isn't really a one size fits all perfect automatic solution. Not all apps are good macOS citizens.