From this Artima article on clone vs copy constructor:
Object's clone method is very tricky. It's based on field copies, and it's "extra-linguistic." It creates an object without calling a constructor. There are no guarantees that it preserves the invariants established by the constructors. There have been lots of bugs over the years, both in and outside Sun, stemming from the fact that if you just call super.clone repeatedly up the chain until you have cloned an object, you have a shallow copy of the object.
What does Joshua Bloch mean by extra-linguistic?