Final answer:
Mr. Puncto found discrepancies related to missing documents and their appearance.
Step-by-step explanation:
Based on the given text excerpts, Mr. Puncto found discrepancies related to missing documents and their internal and external appearance. In the first excerpt, the Prefect discusses a missing document and its description. In the second excerpt, the Prefect mentions that Mr. Puncto was waylaid and searched but didn't find the document. These discrepancies indicate that there is a mystery surrounding the missing document and someone might be attempting to prevent its discovery.