Does restoring from Time Machine also bring back issues?

I've been using Time Machine since its inception, and I've often wondered about this, but can't find a definitive answer ....

Let's say you wipe your Mac and do a full, fresh install of the operating system. You then do a restore from Time Machine to get your apps, data and settings back.

If you are doing a fresh install to get rid of issues, does the restore from a backup also bring back the issues that may have been present in your OS? Or does the backup "respect" the new OS installation and leave it pristine?