Most C++ users already know that they shouldn't use auto_ptr objects as elements of STL containers. However, fewer users know exactly why this is so.
The C++ Standard says that an STL element must be "copy-constructible" and "assignable." These fancy words simply mean you can safely assign or copy one object to another and get two independent and logically identical copies. In particular, the state of the original object shouldn't change when it is copied to the target object.
This is not the case with auto_ptr, though: copying or assigning one auto_ptr to another makes changes to the original, in addition to the obvious changes to the copy. To be more specific, the original object transfers ownership of the pointer to the target, and the pointer in the original object becomes null. Imagine what would happen if you did something like this:
vector < auto_ptr <Foo> > vf; //a vector of auto_ptr's
auto_ptr <Foo> temp = vf; // vf becomes null
When temp is initialized, the member vf is changed: its pointer becomes null. Any attempt to use that element will cause a runtime crash. This situation is likely to occur whenever you copy an element from the container. Remember that even if your code does not perform any explicit copy or assignment operations, many algorithms (swap(), random_shuffle(), sort(), and many others) create a temporary copy of one or more container elements. Furthermore, certain member functions of the container may create a temporary copy of one or more elements, thereby nullifying them. Any subsequent attempt to the container elements is therefore undefined.
Several Visual C++ users report that they have never encountered any problems with using auto_ptr in STL containers. This is because the auto_ptr implementation of Visual C++ (all versions thereof) is outdated and relies on an obsolete specification. When Microsoft decides to catch up with the current ANSI/ISO C++ Standard and change their Standard Library accordingly, code that uses auto_ptr in STL containers will manifest serious malfunctions.
To conclude, you shouldn't use auto_ptr in STL containers. Either use bare pointers or use other smart pointer classes instead of auto_ptr (such classes are available at Boost.org).