I wouldn't say because they are the last group the pace of play rule should be waived but the idea behind the rule did not apply in this case...
Also, why would you enforce a rule that is not regularly enforced on the final day of a tournament? There have been times during play where the middle group is a full hole behind (JB Holmes comes to mind) and they never put them on the clock...
In my opinion, poor judgement but what's done is done and I guess you need to adapt.