That's perfectly fine, but you don't mention that in your documentation. Either you handle them or you make it perfectly clear that you don't handle them. This is a very important point.

As for figuring out if a list contains a reference ... what's wrong with grep { ref } @list?

I don't see any particular reason why a report on the the intersection, union, etc., of two or more lists should come back in any particular order.

If you were dealing with sets, then you would be correct. However, if I'm working with lists, I expect that the ordering property of lists would be maintained in every single action. map and grep maintain order. Your functions, to me, are in the same vein.

If I want to find out "Is this item in that grouping?", I would consider that a set operation, if I'm using a module. Sets are intrinsically unordered.

The question also isn't a matter of what position in the list a given item was seen. If you are saying @list3 = intersection(\@list1, \@list2);, I would assume (because it's not otherwise stated in the docs) that @list3 has the elements in the order seen in @list1. Essentially, intersection() would be written as so:

sub intersection
{
    my ($l1, $l2) = @_;

    my %l2;
    undef @l2{@$l2};

    my @l3 = grep { exists $l2{$item} } @l1;

    return wantarray ? @l3 : \@l3;
}
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That preserves the order. If I don't care about order, I should be using sets.

Now, you're wondering what the big deal is - most people wouldn't care. And, you'd be right. Except, some people will and it doesn't cost a lot to make it right.