I'm on 14.04 / Unity.
I can't say how to replicate or which are contingent conditions, but sometimes my mouse coursor is some pixel upper than its real position, so if I click on an object, probably I'm clicking on something that is some pixel down.
This issue go away by itself, I can't say how, after a few clicks.
It seems it happens with specific applications, such as
I need suggestions about how to investigate.