The TinyTree implementation maintains statistics to help it learn the best size for creating an initially empty TinyTree. This includes counting the number of trees that have been created since the Java VM was initialized. This number is held in an integer, and after months of continuous running it can overflow. After it overflows, unpredictable consequences occur; there is evidence that these include an ArrayIndexOutOfBoundsException in the method TinyTree.addNamespace().
The problem was encountered in Saxon 9.1. A patch is being committed for 9.2 and 9.3.