http://download.java.net/jdk6/docs/api/javax/lang/model/element/TypeElement.html#getQualifiedName()

currently says

"Returns the fully qualified name of this type element. More precisely, it returns the canonical name. [...]"

No mention is made of nested classes here. If you are used to working with java.lang.ClassLoader.loadClass(String), you would expect in this program

package p;
public class Outer {
    public class Inner {}
}

for the nested class to be named "p.Outer$Inner". Instead, apt reports "p.Outer.Inner". This is perhaps acceptable (it is the source-code form of the name) if that is what you were expecting.

At least "p.Outer.Inner" is the behavior of JDK 5's TypeDeclaration, not yet tried in Mustang.