From what I'm seeing, it's poor coding. When a player gets hit by an ability X that does Aoe damage, Riot only wanted them to get hit by the ability once. Example : Ezreal Ults a Draven, Draven then gets hit by the ulti and flashes backwards to get hit by it again. The issue is that the damage will not proc twice even though it's in range or the hitboxes are overlapping.
Why?
Instead of coding so that each cast of the ability is unique in their damage, they simply put a cooldown on when you can take damage from that ability again. If they didn't put any cooldowns on this or collision detector, it would make it so that every frame or instance you touch an AOE, it would do the damage again (Liss ulti would shred immediately or every tick from Trynd E would tick with the E initial damage).
Ok, but this is a bug, they still have to fix it. Why not just change the way this works?
I think they are just going to lower the cool down to get damaged by the E just right above the longest E duration rather than rework it for every champion's abilities that applies to this.
This is just my theory of what's happening and what will happen to fix the bug, I don't know if that's the issue exactly but if anyone finds a flaw in my logic, feel free to point it out so I can fix it.