Your newly created ```TrackExtra```s hold ```edm::Ref```s to the wrong ```RecHits```. If you are copying the ```RecHits``` then you should set your new ```TrackExtra```s to point to your newly copied ```RecHits```. 
It looks like using the copy constructor on the ```TrackExtra``` is probably the wrong thing since it also copies the ```edm::Ref<TrackingRecHits>```s as well as the ```edm::Ref<TrajectorySeeds>```