Repro Steps:

1) Create a new page.
2) Create 2 layers in the Master Grid of the page: A 'Button' (Button) layer, and a 'Foreground' (Grid) layer on top of it. For now, do not apply any background to the 'Foreground' layer.

3) Press the 'Run' icon, and hover over the button. Observe how it has a visible 'MouseOver' interaction state.
4) Apply a background fill to the 'Foreground' layer. This can just be a Solid Colour fill with enough transparency to see the button underneath/through it.
Observe how the "Hit Test Visibility" property is unticked (off) -- meaning that in theory it should be Hit Test Invisible and should not intercept mouse interactions.

5) Press the 'Run' icon, and hover over the button. Observe how it is no longer detecting Mouse Input.
6) Return to the 'Foreground' layer, and tick the "Hit Test Visibility" property to "On" (meaning it will intercept mouse inputs).
7) Press the 'Run' icon, and hover over the button.
Observe how it is still not receiving Mouse Input.

8) Return to the 'Foreground' layer, and untick the "Hit Test Visibility" property to "Off" (meaning it will no longer intercept mouse inputs).
9) Press the 'Run' icon, and over over the button.
Observe how it now correctly receives Mouse Input.

Expected Result: If a layer has the Hit Test Visibility unticked (set to "Off"), it should actually be Hit Test Invisible and not intercept Mouse Inputs.

I believe the solution here is to ensure that all new elements created have Hit Test Visibility ticked to "On" by default, forcing the user to come and untick any elements they do not wish to have Hit Test Visibility.