Copying a DS from one DB into another will attempt to bring along any related Tables with it. If the Table already exists in the DB you will see this error, and not be able to copy the DS. This is particularly frustrating when you have more than one DS or FC that participate in a relationship with the same table. The first one you copy will bring along the Related Table. The next will fail because the Table already exists. Copying in the Table will also try and bring along the DS and or FCs related to it, which is why you are seeing duplicated FCs in the DB.
The only way around it I have found is to pay close attention to your order of operations and\or remove the relationships and rebuild them after the copy. TabletotableConversion will get you the Tables without the related FCs and or DS but the Relationship will be lost. Problem also exists with Project Operations which is where I ran into it. After much talk with ESRI on the matter it was decided this is a feature not a bug, so my workaround for the projection of a large DB was either remove Relationships and rebuild them afterword, or just dump them alltogether.
