When executing a Python script as a custom tool in ArcGIS Pro through a Python toolbox or other means, Python will sometimes emit warning-level messages via warnings.warn or logging.warn. These should be interpreted by ArcGIS Pro as warning-level messages. Instead, Pro sees these as error messages because Python outputs these to sys.stderr. This will cause them to be shown on the wrong list in the tool results, and it will also indicate the tool has failed, even though it completed sucessfully. I've included screenshots showing the behavior in the results, as well as a simple PYT with a tool that will demonstrate this issue. The tool does nothing but print a warning, but Pro still claims that it failed to run.
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