I usually hit this when making parts (with an error in the part) that crashes Fritzing. It isn't too good about deleting files on failure (or for that matter when deleting parts 
). The cure I use (which is somewhat extreme) is to delete the 2 user data directories and start again. Note well this has the effect of deleting all of your Fritzing projects so make sure you have a good backup before trying this. On Windows the two directories are:
c:\Users(Win_user_name)\My Documents\Fritzing and
c:\Users(Win_user_name)\AppData\roaming\Fritzing
(at least this one is a hidden directory so you need to have enabled show hidden files in explored to get to it) If you move both of these aside by renaming them to (for instance) Fritzing_todays_date) Fritzing will recreate them both. You can then reload the parts and projects and the message should disappear. Note that is you have a lot of files/projects loaded this will be a pain in the ass! It may be possible to look in the data directories and find the duplicate part (which is likely what it is complaining about) and delete just that file, but thats a fair bit more complex to do (and you want to have a good backup before doing any of this as data loss is possible).