When I initially wrote "I have no idea what ', [1]' is supposed to mean.
", you should have believed that and explained ;-). I now understand that most index entries have one link, which we might call the [0] link. When the entry should have more than one link, the index entry text is followed by '[1]' and, if needed, '[2]', '[3]', and so on. These place-holder labels should each have different links, or should not be there at all.

So "ZipFile (class in zipfile" and "[1]" are two separate texts that should have two different links, but the two links are the same, and that, I agree, is wrong. Another example with duplicate links:
  tracer() (in module turtle), [1]

3.1.2 and 3.2a2 indexes have Zipfile error but not tracer error (because '[1]' is not present).

Doc people: the attached patch is a diagnostic patch rather than a fixup patch. I do not know whether the problem is in .rst sources or Sphinx.