Corrected entry: Jen reads (as he learned to do from the Mystic who raised him) the hieroglyphic prophecy, and in doing so, gets a "mission briefing." The problem is, the Mystics understand all of this, so why didn't any of them tell Jen these things as he grew up, or if nothing else, right around when "his" Mystic died and or before he set out for Augra?
Corrected entry: Note: Spoiler. The "good" race is said to be dying, while the "evil" race is flourishing. As the ending makes clear, each individual of each race is really half of one split individual. Thus, there must at all times be precisely the same number of individuals in each race.
Correction: Flourishing here seems to mean wealthy as opposed to population numbers. The "bad" race (Skeksis) were using the life force of other creatures in order to maintain their lives. There were no children shown of either race shown. This is not a mistake. Both races were dying. Did you see any children Mystics or Skekses? Also, the crystal had to be "healed" by the time of the great conjunction. It is possible that if it weren't healed, that the personalities would be separated permanently and therefore the Mystics would die and the Skekses would flourish.
Corrected entry: When the evil Ritual Master calls for the crystal bats to fly away to watch Jen and Kira you can see thin white strings as the bats fly from the castle ceiling.
Correction: Copied from IMDB.
Correction: Spoilers: When the Urskeks split into the Mystics and the Skeksis, each half got certain character traits. The Mystics were peaceful and kind but had but no drive or ambition (which the Skeksis had plenty of). So it just did not occur to the Mystics to teach Jen what he needed.