Ii noticed this and while you may know alot dont so ill mention this. Once you stun a champion and they become u stunned they have a white glow around them and they cannot be stunned again untill this has disappeared. Its mostly a timing issue I think from what I saw.
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Yes thats the mechanic for them, but OP isn't talking about that. He's talking about when the mechanic doesn't work, which is a big glitch in the game, I've seen it many times where they physically won't stun from overload rounds, even divinity. Same goes for barrier Champs, I did a solo lost sector the other day and had a barrier Champ continue popping his bubble every 2 seconds and wasn't stunning (was forced to perfectly time a thunder crash). It's usually not too big a deal for good players, as we can adapt, but lower skilled or powered players might not be able to counter it