When I'm on a Category page (via archives.php template), my navigation menu changes - it appends the category name into the URL. Same with Tag pages. On other pages, the menu is correct. I have my permalinks set to /%postname% with no Category base or Tag base set.
For example, normal menu URLs:
example.com/about-us, example/contact-us.
Once I navigate to any category page, the menu URLs change to:
example.com/category-name/about-us, example/category-name/contact-us.
And note, those categories aren't the categories of those pages - it's whatever category I happen to be on at that time.