I was in a dog fight with a wanted pilot. I am fighting him and once I destroy him, Federal whatever, blow me out of the galaxy.. what gives with that? I wasnt wanted or carrying any contraband...
System authority vessels are faction members too and they put their faction loyalty ahead of their law enforcement job. Your target was a member of the same faction as the SAV that attacked you. Their faction obviously didn't issue the bounty on the wanted ship so they don't care about it and the SAV was retaliating for the "unlawful" murder of his faction buddy. Check factions under Contacts in your left UI.
With other ships I would agree with this but I think SAVs should be different as defending yourself gets you wanted which is a bit unfair really.
Wanted status is not black and white. An NPC might be wanted in another jurisdiction but "clean" in the one you're at. Also... attacking a wanted NPC before you've completed the scan to know that they are wanted is considered a criminal act... so let your scan finish before pulling the trigger.