Doxygen does not appear to understand dereference operators (->) in a templatised class as is typically used in smart pointers.  I have encounterd the problem using boost::shared_ptr, but the following code illustrates the problem:

template <class T> class SmartPointer {
  public:
  T *pointer;
  T *operator->() const {return pointer};
};

class A {
  public:
  void do() {};
};

class B {
  public:
  void do() {};
};

class C {
  public:
  A *a;
  SmartPointer<B> b;
  void do() {
    a->do();
    b->do();
  };
};

The doxygen output shows that a->do() is a reference to A::do(), but b->do() is unrecognised.  This means that member function "Referenced by" lists are incomplete.