This test checks for identifiers of amino acids where the stereochemistry is not defined, e.g. DL-serine.
While most amino acids involved in metabolism are the L-form, D-form amino acids can have specific biology.
If this report is a false-positive, look up the specific biology and decide if the pathway involves the L-amino acid (more common) or the D-amino acid (less common).
A useful approach is to follow the enzyme identifier to the UniProtKB and check the Rhea record for the enzyme. Frequently, Rhea has the stereochemistry well-defined.