I think the issue is unrelated to py.test - it just presents a use case
as it wants to run 1000's of tests and capture stdout/stderr per each
test function, cannot guess about a test's logging-usage yet wants to
minimize memory/resource usage and close any temporary files it opens.  

Anyway, a standalone minimal example involving the issue is this:

import logging
import StringIO
stream = StringIO.StringIO()
logging.basicConfig(stream=stream)
stream.close() # to free memory/release resources

At exit logging's shutdown() will try to flush/close resulting in an
exception.  Is it a problem to have the logging module be a bit more
defensive and only try a flush/close if the stream isn't already closed?