All popups animations swallow mouse clicks, preventing you from clicking on what is below them. This is true for rainbows, numbers, icons, all of them.This is especially annoying because they usually pop up right where you want to click next because you are harvesting a tree twice or nibbling a pig twice or whatever.
But devs, this is an incredibly easy fix! If you don't want a popup to swallow mouse clicks, you can just set the mouseEnabled and mouseChildren to false on the MovieClip for that popup. I submitted a ticket three weeks ago, so I'm posting here in the hopes that it will be dealt with. Depending on how you do these popups, this might literally be a two-line fix.
It would really make the game a better playing experience.