I solved my problem fixing the scale of one Node.
Look at every Label at your problematic scene, probably the error only shows on a specified scene, at least it happened to me.
If the Node is with the both scale axes on 0, set to another number.
The error just desapear after changing this. (And back when i put (0,0) again)
In my case, was a Label scale(0,0). It will look like the problem is when changing scenes or the problem is with a node visibilite (Cause when you hide the parent of the actual problem node, the error stop showing on Debug), but the real problem is with the Scale of a node.
*If both Scale axes of a Label Node is == 0, or even one Axe is == 0, the error will show.
The same error apears in both Versions (Don't know if apears on more):
Godot 3.2 Alpha 2
Godot 3.2 Beta 2