While playing after upgrading to the Factory floor, the game also placed the Rail lines and chests on factory floor as well as unlocked the Harvester floor and the Teleporter. The rail markers on the "planets" layer disappear on warp but reappear on any Warptorio upgrade.

The only option I have enabled above normal is the early water for boiler floor.

I already found out that enabling early water can cause this issue. I am trying to fix this, but first on my list is to find minimal size needed for yellow science + rocket silo. So after that update this bug will be fixed