There are two symptoms of this: the Applications menu reaches beyond the size it can on a single monitor and off of the border of one monitor, and the workspaces are placed such that 90% of a workspace may display on one monitor and 10% on the other (or 50/50).

To duplicate:

 * Have two monitors.  In my case, they are not the same size; I have a 1440x900 monitor (primary) and a 1280x1024 one (secondary) using TwinView.

 * Press the Super key, or otherwise trigger the workspace overview/search/application/etc. screen.

 * Click "Browse" on the Applications pane.

 * The menu will be the height of the tallest monitor (1024) and slightly wider than the primary screen.  Of course, depending on the resolutions and arrangement this may be different.

It might be worthwhile to figure out how Mutter and the old gnome-panel determine the size of the screen it's displaying on, and then adjust the menu display code for the Applications menu and the workspace viewer so that the menus do not cross monitor boundaries and the workspaces themselves do not cross monitor boundaries (which of course means that if there is only one workspace, it should only display on one monitor or the other (or the other..., etc.).