Before 0.14.0 it was fine to overlap within the same layer based on order but 0.14.0 will randomly overwrite contested space with which ever. So now you gotta be smart in using layers, and frankly distribute to more layers and waste more memory.
I wouldn't recommend to use the special layers like walls stencil, fire, light, and indicators since that could become messy. Do it if you must and know what you are doing.
Alternatively, you can create more layers in exchange for a spike in memory use and lag. I wouldn't do this unless you got tons of stuff needing it. I got tons needing new layers but still have decided to avoid it even if there would be graphical glitches. Because frankly graphics isn't so important when you play but functionality is.