NOTE: I solved it, my issue was that my HBoxContainer Mouse filter was not set to Ignore. This made my buttons work now, but knowing of an easy way to break on any mouse click and follow it through would be useful
I have a GUI scene, with various containers for layout. This scene is instanced inside of a game scene, which has a viewport container, viewport with the game stuff, and the GUI as a sibling to the viewport:
GUI:

Game scene (with the UI highlighted):

Screenshot showing buttons along the bottom:

My issue is that clicking on the buttons does not work usually. I think the BoostButton can be clicked sometimes, but have not been able to click the CCW, CW, or Reset buttons.
I have a basic understanding of input handling, but it falls short of helping me debug this issue. I'm familiar with the built in debugger for gdscript. Is there some way to use that debugger to break on any mouse click input and follow it through to see where it is being handled? Is it possible there is some object in front of the GUI that isn't letting the click through to the buttons?
Any help is appreciated. Thanks!