I've had the installation of apt-get packages permanently hose an ubuntu or debian install. It's all up to packagers to author their packages right so they don't leave garbage on your machine that you have to manually clean up (or give up and reformat).
You're comment is very light on detail so it's hard to understand your issue properly but I've been running Linux as my primary desktop for more than 15 years and have managed literally hundreds of Linux servers too and never had a package manager hose my platform (big caveat: aside the notorious `filesystem` update on ArchLinux but that one is an extreme edge case scenario due to the rolling release nature of Arch. However even package was well documented on Arch's site beforehand as being a package that required manual steps to upgrade).
It's true that Linux package managers used to be buggy and problematic in the 90s but those days have long since gone. And while I'm not discounting that a package upgrade could damage your system, the instances when they do are highly unusual rather than a typical problem users face with each and every upgrade. In fact Windows sysadmins have far more dread with running Windows updates than Linux admins do and yet Windows updates are only focused on Microsoft products rather than every piece of software on the system.
> It's all up to packagers to author their packages right so they don't leave garbage on your machine that you have to manually clean up (or give up and reformat).
Actually it's not. It's up to the application developers to do that. If you specify a package to install a file `x` to location `y` then the package manager will uninstall that file automatically too. You don't specifically need to tell the package manager to do that (or at least not with any of the packaging systems I've used). But if the application developer writes the application to spew out thousands of files into $HOME, that happens outside of the package manager. There isn't a whole lot you can do to stop that aside limit the directories which your application has permission to write to (either via chroot, containerisation, user/group permissions, SELinux, or other forms of ACL. There's actually plenty of tools on Linux / UNIX to handle that problem).
Don't know about apt specifically, but using pacman (Arch Linux), you can list exactly what files on your filesystem were installed by what package and remove them. You can't do this on Windows, as far as I know.
