List of common mistakes done when making interiors:
Weapons and Armor:
Always check them. Most of the float at one point by default.
misc_com_wood_knife: This floods by standard. Notice the wooden part of it. While one part of it will touch the surface when using "f" the other will not.
Moldcave: Is supposed to be stone, so don't let anything bleed with the ground, wall or roof.
Stuff with planks: Most of the time the plank are always uneven, be aware of that.
Ashlander Yurts: Ground is non-flat.