Well, let's get in position. This permission is important and what I read in Marshmallow not prompted the user with a dialog box (as we are asked some now for the first time), but you have to give us the app, so Google considered important to create a specific section for it.
Now when you get a message saying that you need a permit if it is a 'toast notification' (the lower that are shaded in dark), it is likely that the app that you need is not where you're at that moment, but one that was intended to appear above the current. This is something like:
You're in an app anyone, you get a message from a Facebook chat and instead of aparecerte your bubble, you get a message like you say. That would mean that Facebook needs permission to overlie the rest.
I've been reading and that's what I understood. So if you have any app that usually shows bubbles (musiXmatch, for example) or any other such thing, look to see if you have the permission enabled. If you do not know, go trying discard.
The second catch is filtering apps that do have the permission enabled, but not all have it activated.