Have you by chance been radiant when this happened? I stumbled over this too (see below). When the Bungies communicated that we shouldn't be able to stack multiple anti-champion capabilities on a single weapon (after the latest subclass verb addition to anti-champion stuns) they specifically mentioned chill clip as exception to that rule that should always work. Yet apparently this behaves strange. I noticed this when farming in Concealed void: While I was radiant, Chill clip would stop the overload champion from regaining health but it would not stun him, but would work fine if I let radiant run out before engaging him.