This problem's output validator does not treat its output as a set. My solution is
checkio = lambda first, second : ",".join(set(first.split(",")) & set(second.split(",")))
which yields
checkio("one,two,three", "four,five,one,two,six,three") =>
'one,three,two'
on my local Python interpreter. However, on the web app, it returns some other permutation of the correct answer, yet it is marked as a failed test case.
From: http://www.checkio.org/mission/common-words/solve/
HTTP_USER_AGENT:
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/601.2.7 (KHTML, like Gecko) Version/9.0.1 Safari/601.2.7
Created at: 2015/11/02 07:00; Updated at: 2015/11/02 11:27