I have a MacBook Pro 17" mid 2009. As a developer I have been running El Capitan since Beta and am currently running 10.11.2.
The problem I am having is application windows lose focus. In simpler terms the window is visible but becomes inactive. It is a pain because if I am typing like I am typing this, when the Safari window becomes inactive I am unable to continue typing and I get an error sound. It seems to happen every 3 to 5 minutes even when I am actively using the application window.
Is anyone experiencing the same thing? Does anyone have a solution? It is a really annoying bug!