>  When I say $document[1], it considers all files as $documents[1].

This is not possible. There is no data value in xpath that corresponds to
multiple documents except a sequence of document nodes, and as you can
not nest sequences, it is not possible to return a sequence of more than
one item as a result of $documents[1].

What expression did you actually use to give the impression that 
$document[1] is all files.

David