Issuing query like [1] causes an exception in PrestoDB. This seems to be PrestoDB issue. I found similar issue [2], but that one should be fixed. I have created a new issue [3]. Removing one column from ORDER BY, query returns correct result.
Not sure if we can do something about it without avoiding pushing JOIN.
I suggest either to fix this (if simple enough) or add a note to the documentation.

[1]

SELECT a.intkey, b.intkey FROM BQT1.SmallA AS a INNER JOIN BQT1.SmallB AS b on a.intkey = b.intkey ORDER BY 1, 2

[2] https://github.com/prestodb/presto/issues/1621
[3] https://github.com/prestodb/presto/issues/7010