You ignore the findings, and submit the report but add an addendum.
Since the inconsistency does not directly relate to the main research questions, you ignore the findings, and submit the report. However, you add an addendum explaining the error, and your justification for discounting its overall impact. These are some possible outcomes:
|  | Response of reviewers is to challenge your justification
|  | Reviewers feel that the findings should be included in the article.
|  | Reviewers feel justification is adequate