exactly sir. ur view is correct. an auditor while reporting, should be aware of the use of expressions in the report. a qualification in the report is to be substantiated in the report or its annexure. the likely impact of the qualification in the financials, if possible should also be explained. Reference to a notes to accounts is a routine practice by auditors. But the reason for such referece shuold be explained in the report.
But the statutory requirement is always statutory. The directors are expected to give explanation to the qualifications in the auditors report. The rite or wrong done by the auditor is not an issue in this regard.
In ur case, i think it is better to have a discussion with the auditor so as to analyse the impact of the opinion of the auditor in the financials and see whether it is to be qualified or not.