I assume you are referring to ObjectDock.
The empty space is probably caused by either an invisible entry (due to dragging files onto the dock recycle bin), or due to a seperator which is not showing and uses the same spacing as a dock entry. Note - at this time, ObjectDock does not support drag-n-drop of files to the recycle bin without also creating a dock entry. Perhaps this will change in future builds.
In the case of an invisible entry, just click on the spot and drag off the dock - if you get a "poof" then that was the issue.
In the case of a seperator which is not showing, you can right-click on it (this may take a bit to find the correct location) - until you see a "remove this seperator" option in the context (right-click) menu. 
Note - you can also remove a dock entry by right-clicking on it and selecting "Remove Entry" from the context menu, which allows you to remove the entry without deselecting "Lock Dragging". 
