In 2.4 for a time, what you say was not the case, except under a certain unusual circumstance which I never did manage to put my finger on (some kills stacked to completely different bases and factions for no apparent reason).
I didn't know this happened with skimmers, can't say I ever saw it, but it wouldn't surprise me, it did happen with data point scan missions, in that sometimes you scan one, and a mission for elsewhere completes, meaning you have to leave the planet and come back to the same one again. This was still happening in 3.0.1 but it doesn't always happen and I don't know if it still can after 3.0.1.