Has anyone found a scroll with the Levitate spell in Stone Prophet? It's listed in the game manual, but I've not been able to find it. I don't see it listed in Strahd's Possession, which suggests that it's only in Stone Prophet.

I can't recall finding it, but Levitate is utterly useless anyway.
It's very present in Menzoberranzan (mainly through potions) and it's even useless in that game.

You're correct in that the spell isn't really needed since Jump and Fly are available. I was curious because it was listed in the game manual and I've never seen it found by any of the players who've posted YouTube videos of the game. I thought it might have been mistakenly carried over in the manual from its use in Menzoberranzan. The clue book doesn't list some of the spell scrolls that are found in the game (Protection from Evil, Spook, Hold Undead) which made me wonder if the Levitate scroll was available but not shown in the clue book.

It is most likely a copy & paste/carryover error from Menzoberranzan, yes. All three games used the same engine with minor tweaks and improvements. And yeah, Levitation itself is pretty useless as you can only move up or down; no forward motion of any kind is permitted, which means the spell is useless as a means of traversal as the maps are still primarily 2D.