Is that the one where you’re supposed to use the bomb on the overhead crane to blow them up? If so, that’s why - the game expects you to follow the side quest script, not short-cut it. Any time you try to short cut any quest with scripted stages, you’re going to run in to the same issue.
Yeah, that mission, but the bomb part doesn’t show up until everyone is dead. When this happens I just kill anyone I see on the way through to the diamond which is only about half of them, hit the diamond, then backtrack to continue killing. Either way, everyone has to die before you can activate the bomb. That’s why it’s weird to me why it matters that you even need to touch a waypoint for kills to count.