As above, but there are other possibilities that do not involve changing the authoring.
There is a move tool just in the top right hand corner (arrow with a compass icon) under the ' File Edit Object Menu ' bar.
Click this then select the icon in the flowchart you wish to move.
If you have unlinked an item completely and it hasn't disappeared in the flowchart
right clicking (Windows) in the flowchart should give you an option menu with 'Auto Layout All' as one of the options.
This cleans up any orphaned icons but also resets your icon positions 
which is a pain on a large project.
I found that if you drag an item from the bottom of the flowchart window into the flowchart, you cannot get rid of the icon
without doing an 'Auto Layout All'. Looks like a bug in this version...
If the item is created in the flowchart by creating a link from the properties dialogue (eg end action) select 'delete' in the same pulldown menu
to delete the link and the item.
Version : Encore CS5.1