The only way I've seen it happen is if you moved/removed/added the hosts to an existing vCenter, did a new vCenter install vs. upgrade or change the names in our data collectors.  We look at the UUID of the VMs for their uniqueness.  I would suggest opening up a support case and have them take a look at a support bundle from the FMS and from the data collector.
Does anyone know what the issue is with vFoglight when it duplicates all of the objects from vCenter?  This is the second time I've seen this now and in discussions with others who run vFoglight in their shop, it has happened to them as well.  Not only is it a complete annoyance, but dashboards made for specific VMs all of a sudden stop working because their new data becomes associated with the new VM object in vFoglight.  I went from 4.4k machines in one vCenter to 8.8k over the weekend.  Is there an easy way to delete the duplicated objects and get data flowing to the original objects again so I don't have to redo a whole bunch of dashboards and reports? 
Duplicate Objects