Turns out I was using CanvasLayers wrong. The simplicity of it confused me so I messed with the settings too much even though it would have been better if I left it alone. My scene tree to popup was
- Player (KinematicBody2D)
In CanvasLayer I had Follow Viewport enabled. That was what was wrong. I just needed to leave all the default settings alone.
Thanks for the info about popups. Now I know how they work and a bit on how CanvasLayers work.