This happened with us during a space exploration playthrough on factorio 1.1.104, with a bunch of mods (most notably minime as recent trouble maker), everything up to date.
What happened? I was in a spaceship, it was stationary at Nauvis Orbit. I opened Factory Search and tried to update the query from Request:space_elevator_cable to Product:pipe, and upon a button press (I don't remember which, either the pipe or a checkbox) the server crashed (see logs below). (I might have been running in really fast armour and it is possible to then move through the walls of the spaceship, idk how surfaces work in SE but this might have caused a surface to become null and hence the error. Or maybe the spaceship was launching or performing a check or something else and that somehow caused something with the surface-ids. Or maybe I was exiting or entering god mode with minime but I am fairly certain that a debug message would have been printed by minime if this was the case. I hope that some proper checks can prevent future crashes like this.) I hastily tried to reproduce this in single player but I could not crash the game.
Log file: https://pastebin.com/uyMRuEkt
Excellent mod by the way, we are really satisfied with it.