The problem happens when the component resides up the map. Another version of the component is added and referenced by a program in the entry stage. Both elements are moved up the map. The original version of the component is added into the entry stage. The intermediate version is copied back from up the map, creating a new version. Both elements are moved up the map and placed into a package. Component validation fails since the footprint on the component does not match the original up the map.
There is a Agile story to have this functionality changed. Check with support for the availability of a fix.
Regenerate the element in the current location.