Hello everyone, mostly legend player here. I know that enemies that are stuck in movement animations cannot be knocked out of it unless they are killed, and that they take +40 % damage ( because they are considered staggered twice iirc) since the stagger update.
This is how it has been since the game has been out.
However, I’ve lost count of how many times I’ve been near a ledge, hit a foe, and then immediately got hit back because of that stagger invincibility. It happens quite easily with slower weapons and chaos foes (or elites) because they might not get killed by the previous hit, and so you get hit between weapon swings. That problem is especially apparent when you hit them right before they finish their anim, or when you make the mistake of standing below a ledge that enemies can drop from (then you get surrounded and attacked almost instantly).
In that other zombie game Back4Blood, for all that it does wrong, that issue was solved with a simple fix : when you hit a foe that’s very close to the end of their climbing/jumping animation, the hit-stagger anim is queued right after. There’s a small delay, but the stagger anim still happens. It was “stored”, in a way.
Imo, I’d be ready to sacrifice some of the damage bonus to climbing enemies, and instead get a more reliable way to stagger them. It seems stupid to me that enemies locked in movement anims are so much more dangerous than the others. Also, it would make the slower weapons feel more impactful in specific situations.
Just a suggestion 
I just thought of this topic in a legend game a few minutes ago, with Sott and the Repel talent. Made the mistake of using it against foes dropping from a ledge. I was so used to blasting them away, and I was kinda dismayed when nothing happened.