I have three desktops (plus dashboard) set up with Mission Control, with certain apps assigned to each desktop. If I minimise a window with Cmd+M in one desktop, then whilst focussed on another desktop restore that window using F10 and selecting the tile, the window restores to the focussed desktop, not the one to which its app is assigned.
I have replicated this with both Apple (iTunes) and 3rd party (Chrome) apps. Chrome has an even stranger behaviour - restoring the app to the wrong desktop, then automatically switching focus to the correct desktop (without the window in it).
The issue does not happen when I right click on the app icon and restore the window from the menu there.
Late 2008 13" Macbook, running OSX 10.9.1 and latest versions of all software involved.