I am using a few QOL mods and there is one designed to affect walls so that might be it: https://mods.factorio.com/mod/no-stone-wall-alarm

I don't place ghosts in these cases, it's only when they're automatically rebuilt by bots/platforms.

I'm using legendary walls on my Nauvis base as well as on some spacecraft. I've noticed that when a legendary wall is destroyed by biters or asteroids, bots (or space platforms) replace that wall with a normal quality wall instead of the original legendary wall. I haven't noticed this inconsistency ...