Are you sure you're killing the right faction?
I don't know, if it is a bug it's not a consistent one because I just finished a CZ mission. …
Yes, it was the right faction.
I took the mission, went to the combat zone (after logging around a few times to spawn a combat zone - other problem), joined my faction and started killing enemies.
I got the bonds, the blue notification that I got the bond and the kills counted.
Until they didn't count anymore.
The enemy ships suddenly didn't have the "mission target" indicator. I got no bonds (checked that) and I got no additional kills. It stayed at 9/16.
The BGS tick happened while I was in the CZ.
I went back to the station, restocked and checked the faction influence. Went back to the CZ and started killing enemies again - this time it took 2 kills before the kill counter changed and afterwards everything was back to normal.
Very strange.
My current suspicion is that the BGS tick might have caused this as the faction I work for "won" the war early (Influence difference is higher than 15% after two days of war and one day min duration to go). Maybe that caused the confusion of the mission.
(Yes, missions look very bugged currently. Bizarre low payment for elite missions, stations that offer a lot of missions of the exact same type and only that type of missions, stations with 0 missions…)