Guess - Turreted weapons set to "target only" may be fired prematurely by pressing the trigger immediately after selecting a target resulting in a bounty. When set to "fire at will" the weapons will only fire when they are good and ready.
TL;DR
Tested this out yesterday (17/2).
Went to a low res site in my Type 10 fitted with turreted weapons only. Set them to "fire at will". Pirates who scanned and fired at me were destroyed. My weapons did not fire until the pirates did. No bounties or fines gained. I then set them to "target only". Pirates who scanned and fired at me were then selected and destroyed. Again, generally speaking, no bounty or fine gained. However, on one occasion received a 127 Cr local faction bounty for assault on a pirate who was attacking (or threatening to attack) me. I was then attacked by system security ships and destroyed before completing high wake [ouch!].
My guess. It seemed with turreted weapons set to "target only", I could fire on a wanted NPC prematurely. So, for example, if a wanted NPC starts attacking, but you select the NPC and return fire immediately, the game may see this as you attacking before completing a scan. I would stress this is a only guess, but normally a scan would be required. In contrast, when my weapons were set to "fire at will" they fired only after the NPC fired at me. In some cases not at all, even when the NPC had scanned me and was being attacked by system security, because the NPC didn't actually fire at me. Anyway, have submitted a bug report with my results as Sandro requested.
Has anyone else fiddled around with "target only" mode? Would be interested to hear from players using "target only" mode to confirm the exact mechanics (selecting, scanning, firing etc.). This mode may in fact require more pilot care than fire at will, but I'm not sure ATM about my conclusion re need to complete a scan before pressing the trigger.
UPDATE: Went back to a hi res site today (18/2). Different ship, but all turreted weapons. Stayed for 2 hours. "Fire at will" for 1 hour - worked without incident. If anything, had trouble getting the pirates interested despite a "tasty" cargo. Then went over to "Target only" for 1 hour. Made sure the NPC was scanned before opening fire and made a thorough nuisance of myself getting in the way of the system authorities - again, worked without incident.