I have various Apps set up in spaces: Finder in (1), DTP progs in (2), Mail in (3) and Browser in (4). Sometimes when I'm using an app with an open document I switch to finder or mail... then when I switch back the app is there, but the open document has disappeared.
The App tell's me the window is open but I cannot bring it up, I have to quit the App then re-open to bring the document up again.
This hasn't happened to me, but on occasion the background of my dock will disappear. And the rounded corner backdrop of App names (shows during mouse over) disappear. Only after restarting will the issue go away.