Inspector_gadget told me this happened to him before... It just happened to me. +1 Evil Wells map with no wells on it:
Ran this map:
Godly rawhide electriver map, +3 Warm Lights, +3 Evil Presences, +1 Rooms, +131% Warm Light Effectiveness, +4% Level Up, +2% Stealth, +1 Evil Wells
My thought is maybe the Evil Well spawns on the last square but is replaced by the uber treasure chest?
Or maybe something else replaces it like an evil presence?
I ran this copy because I only managed to well ~25 items in my last 5 wells. But this was way more sinister than a well that poofs in 1 item