(Seen on Switch v6.5, in handheld mode)
And with video footage, too: Gems of War bug: "Stairs already used" - YouTube
So my incident here appears to be harmless (I had already cleared the dungeon for the day, and was just checking off the remaining doors), but the error message appearing at all is the mystery.
Other detail of note: it looks like I tapped the “Stay” button twice before the prompt disappeared. Could this be relevant?