Some textures are removed on saving map.

[DEKiMA]

Anyone know why this is happening or how to fix it? I'm not sure why, but after I edit some textures on my map to different ones, once I save it reverts parts of the changes. Here are screenshots which I think will explain better. It's always in the same pattern, and this happened on another map I made where the same concept was being used. If this was still too vague, just ask me and I'll try to rephrase my question and description.