Getting frustrated with missions

Hello all,

I don't understand this mechanic and quite frankly is getting me frustrated to the point of putting this game on hold for awhile. The factions and how they relate make no sense in this game. The issue I have is sometimes I get a mission for a federation navy rank advancement to kill someone. Fine. After I kill the person, I get a bounty, huh?? Then when I go back to the station I got the mission from they blow me up, ??!?!

Am I missing something here?
 
Some missions are "Black Ops", meaning they want you to take the fall for the good of the Federation and the right way of Life *shifty Eyes*

Honestly tho, I figured that Black Ops missions are just that /shrug.
 
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