Product and version FMPA 220.127.116.11
OS and version OS X 10.10
Layout script trigger icons in the lower right of the layout render over over other objects while editing in layout mode.
How to replicate
Add a popover that extends over the Layout script trigger icon
This is slightly expected behavior. You would want the icon to render over most objects on the layout. It does not seem intuitive that it renders through a popover that covers the icon while working with the popover in edit mode. I spent a little while trying to figure out why there was a trigger icon in the middle of my popover. Feels buggy even though it is of not large consequence once you realize what it is.
I have attached a screenshot with some transparency added tot he popover so you can reference the lower right corner. You can see the hide icon next to it does not show through, but it is tied to an object and not the layout itself.