New Network Administrator Needs basics

I’ve been thrust into a network admin position. How do I control who has access to a server? I have set users accounts and established permissions, but still find unathorized users “piped” onto or through my server. These UA users do not appear to be using resourses, but I can’t explain it successfully to anyone, or myself for that matter, as to why these other users are showing up on the security audits.