With ordinary objects such as algebraic expressions and lists, Maple is careful never to have more than one copy of the same thing. However, with arrays, tables, or procedures, things are quite different. When you put them into a set, no duplication is detected so the set has two members. If tables, arrays, functions, or procedures have been created separately then the addresses pointing to their data structures are different even if the data structures themselves are not. Thus the kernel routine that removes duplicate elements from a set will recognize them as being different in this case.
Set operations seem to distinguish distinct invocations of arrays.
Set operations do, however, handle lists and lists of lists as expected.