Similar to this, but the behavior I'm seeing is even stranger.
I'm encountering some very frustrating behavior on El Capitan using multiple monitors with separate spaces for each monitor. When I cmd-tab between one program and another that has lots of windows scattered across the spaces (e.g. Chrome), sometimes OSX doesn't select a window of chrome that's visible on one of my two monitors - it goes and changes spaces for no apparent reason. It does change to a space with a Chrome window open, but it doesn't even select that window. I don't know precisely how to reproduce this, so I was wondering if anyone else had observed this behavior, and whether anyone knows how to fix it.
I know that disabling "Enable separate spaces for each monitor", as suggested in the linked question above, will eliminate this problem, but having separate spaces for my monitors is a big part of my workflow.