It looks like ArrayStoreInstructions type checking is incorrect. The following code causes JPF to throw an ArrayStoreException from ArrayStoreInstruction.java:72.
Object[][] o = new Object[][] { new Class[0], new String[0] };
I looks like the type checking assumes that the array will only be one dimension so it figures the component type is [Ljava.lang.Object (instead of Ljava.lang.Object) which is not a supertype of Ljava/lang/Class.
My quick fix is to add this code:
while(arrayElementCi.isArray()) arrayElementCi = arrayElementCi.getComponentClassInfo();
after line 66 in ArrayStoreInstruction.java