I want this more polished version of the game ahah!
I think the bug occurs when dark and darky collect the upgrade in the same time, or when you re-enter in the upgrade when the vfx is taken.
The simplest way to fixed would be to disabled the collisionshape of the upgrade when you collect it:
$CollisionShape2D.set_deferred("disabled", true)
(need to call set_deferred to be called in the end of the physics loop)
Viewing post in Darky & Dark jam comments
It's a plugin called Post Process I found in the Asset Library. https://godotengine.org/asset-library/asset/2604