How to prevent User Roles from getting reapplied? For whatever reason when I remove a role from a user's profile, at url site/user/user-id/edit it just comes back a few days later. I tried to check users_role table but I do not have that table.

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We do import every employee every night, based off Active Directory, but I do not touch their roles in the import. 

I imagine the best way of solving this is finding the table that has every user's roles, then just removing that entry from the particular user.
Try to run this: show tables like '%role%'; MySQL statement. In the results returned you should see a users_roles table (not users_role). To that table's columns are stored the uid and rid, therefore you will be able to find all users that have assigned with a role or more, and possibly an answer to your question.

I would kindly suggest you, since those roles are appeared again and again, to search any by chance or forgotten user_save implementation within your code.

Hope this help!