How do I Make an object not pass clicking and array?

I have an event that brings up a popup window to allow the user to click yes or no. Unfortunately for me this window pops up over other objects that have events on them. So when I click no, the conditions for the object under go off. Is there a way to make the popup window stop clicks going to the bottom object? they are on different layers.

The problem I am getting is the bottom layer fills an array value so when the user clicks no or yes; it is adding another value to the array. I have tried to use different things with arrays to delete the index thats added but I have had no luck. Maybe its because i cant delete the only entry? I have tried destroying the array and recreating it but it is still populated.

Typically you use Groups to manage your inputs. Place the relevant input events in a group and toggle it off when your "window" pops up and turn it back on again when done.