I had my #1 overall pick promoted from Rookie to Low A today and it was not done by me. There's not even any way it was done by accident. I do have AI controlling my Rookie League, but I wasn't aware AI could make promotions. Has anyone had this done before?

If you have the AI managing your disabled lists, this can happen.

As in my Low A roster got too low, so they called him up? I'll have to check on that

Likely....
Manage Disabled Lists? - Checking this box will indicate to the game's AI that the it should be responsible for placing injured players on the appropriate disabled lists as well as activating players when healthy. These types of moves typically result in player promotions/demotions and/or the removal/addition of players to the Inactive List. These roster moves then trigger the other AI pieces to be used (if the AI is checked to do so.) You may select to have the AI set roles for all of your minor league pitching staffs, any of the five levels (AAA, AA, High-A, Low-A and Rookie Ball) or any combination of the levels.

NEVER let the AI manage your minor league disabled lists.

Thanks for the tip. I had no clue they could promote players. Especially since my Low A roster was only at 23/25 after Shermann went on the DL, with an inactive player on the roster. Hardly "panic and call up a player" territory. I'll start managing those DLs myself though. It should be more clear that AI can do that.