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You will be able to see stderr in the log file if the extended object returns a non-zero exit code otherwise, it is ignored. Anything sent to stdout is interpreted as part of the extended object.
Also note, if an extended object returns non-zero then your job will show as a failure in the GUI.
So as an example, this would produce an error in the log file if gathered in an extended object during an audit:
echo "this is an error" >/dev/stderr