When upper floors are hidden, multi-floor buildings like the stacker hide the upper parts of their model. However, their hitboxes for clicking are kept the same, meaning the player can accidentally select/delete buildings when the mouse is over the hidden parts of their model. Belts/buildings on floors higher than the current one do disable their clickboxes when they're hidden, which leads the player to assume anything hidden is unclickable, but that isn't actually the case so they've been set up to accidentally delete buildings they don't intend to. Belt elevators feel especially incongruous, as their hidden upper parts remain selectable right next to the unselectable upper belts they connect to.
The images show how the stacker and elevator have a selection ghost (and thus can be selected) when their hidden parts are moused over, but the hidden belt doesn't.
Expected behavior would be for building clickboxes to be adjusted when their top areas are hidden, so the stacker for instance would only be selected/deleted if the mouse is hovered over the bottom section, not when hovered over the hidden top section or the pillars (as upper level belts/buildings aren't selected by clicking their pillars either).