So when you get Conflict Zone missions such as "Massacre <insert faction>" you need to go to the Conflict zone and set your IFF to one of the two factions in conflict.

It's on the right-most tab of the right-hand menu (Functions I believe). First option should say [Choose Faction] Double check and make sure you pick the right faction. At that point all your radar contacts will turn Red / Green.

Second. Any kind of bounty-hunting outside of conflict zones involves that you use your scanner to identify the target as wanted. Even if you're in a Nav Beacon or RES and there are 4 Fed-Sec pounding on that pirate. YOU need to have scanned him or you'll be guilty of an unprovoked attack.

You can either target the beacon and scan for the objective or you can run a Discovery Scanner from Supercruise to achieve the same result.

"Assassinations" Are IMO more trouble than they're worth. Massacres and Conflict Zone stuff are good work. If you need to kill Pirates go to Resource Extraction Sites. RES will almost always spawn in the rings of any ringed planet.