The "Copying files" dialog is missing some X11 window hints that indicate to window managers that it's a dialog (and not a normal window). As a result, tiling window manager treat it as a normal window, and will make it fullscreen/split the screen, instead of treating it as it would other dialogs. This also has some minor efectos on other types of window managers - compiz will not treat it as a dialog either. I compared the output of xprop with other dialogs, and it seems the property "_NET_WM_WINDOW_TYPE" should be set to "_NET_WM_WINDOW_TYPE_DIALOG" instead of "_NET_WM_WINDOW_TYPE_NORMAL".
Yes, it is very annoying in tiling WMs, especially when files are copied fast and the WM just resizes everything for a moment and then back.
Duplicate, see bug #11467 (with patch). *** This bug has been marked as a duplicate of bug 11467 ***