There may be more issues when https://mods.factorio.com/mod/Krastorio2-spaced-out/ is used together with Crushing Industry

This is an old compatibility setting. You can disable this in the mod settings. I don't currently handle proper K2 compatibility, as it takes a significant amount of time I haven't had to invest. I would like to eventually! But I'd advise disabling that setting for now if it doesn't do what you want

It is enabled however. It's something to do with the combo of K2so + AAI Industry + Crushing Industry

That change is actually made by K2 + AAI Industry, independently from Crushing Industry

then glass shouldn't be removed when only those two are loaded, don't you think? - but it's only happening with the combination of those 3.

Do you still have the setting enabled in Crushing Industry? If you do, and you don't want that behavior, then turn it off.

OH. I didn't notice the setting for glass. Problem solved by disabling that.