I have had a series get dropped for some reason, but I assumed it was just the EPG people screwing things up and it's easily fixed.
They give a different series link ID to different "seasons". So if they run S1 and S2 concurrently your series link will silently drop and not record S2 unless you set a new series link for it. This happens all the time so check your "To do" list. Another issue is when they split or merge episodes it may fail to record too because they haven't given the new item the series link tag.