This is somewhat rare but not impossible. The applicant's timeline would have given a clearer picture. Besides, most Nomination Certificates are valid for 6 months in the first instance. Although the post is a bit unclear, it appears that the initial Nomination Certificate had expired and was extended prior to the submission of the application referred to, but IRCC somehow missed the Extended Certificate (since no LOE was included). I may be wrong but my best guess as to what happened will be that the initial application submitted after the nomination was rejected late (almost 3 months after submission) due perhaps to incomplete documentation. By the time the applicant got another ITA (could also be paper-based) and was ready to submit a fresh application, an additional 3 months had almost lapsed with the initial Nomination Certificate expired. This informed the extension, after which the new application was submitted but unfortunately the new development was missed by IRCC. This is just my assumption. Will be good to get a clearer picture from the poster.