I know it's an old question but I ran into this problem also and maybe it could help all the other that will have this problem. As you said you only REMOVED the table from the EER diagram and not DELETED it. In order to fully delete this table look at the left side pane under "catalog" you can see all of the tables you ever created including the ones you removed, The not bolded tables are the ones which you only removed. The only way to delete them is to DRAG them back to the table sketch view section and then right click to delete.
Now when you'll output the script you won't see those old tables any more.