It sometimes happens when windows popped up from IM or nautilus
(eg when a device is inserted) on another workspace that
Alt+Tab lists the window(s) in all workspaces even though they
are only in one other workspace - they can make them hard to
find if one has a bunch of active workspaces...

I can try to describe steps necessary to reproduce if it helps.

This is a pretty long-standing bug and finally annoyed me
enough to file a bug.

(Once the window(s) in question have been made visible (given
focus) of course the problem goes away.)