I've noticed this since 3.0 but I don't think it's really a bug. If I understand correctly what you are trying to say, then I believe there are certain scenarios that can cause that:
When your primary targets dies, from a dot damage or something else, before Chain Lightning travels to it, then Chain Lightning goes on cooldown but the instant buff is kept. When you hit someone who has a force immunity, like assassin's shroud or concealment's rolldodge, then chain lightning goes on cooldown but the instant cast proc buff is kept.
I've never actually noticed whether that proc is still displayed on my buff bar or not in those scenarios, but I am pretty sure the next chain lightning is still an insta proc if the buff does not wear off. The idea here is if your Chain Lightning does not do actual damage, then the buff is kept for the full duration
For your particular case, my guess is that some weird bug is going on but you actually obtained the buff, through either thundering blast, lightning strike or force storm, and chain lightning is cast but never traveled to the targets to make the killing blow, in which case you are out of combat and the buff is seemingly "consumed". If that is not the cast, then you just earned a Nobel Prize of Bug Report