If you place a layer of stained glass, and then place another layer of a different color two blocks (or more) above the previous layer. Often the bottom layer will render over the top layer of stained glass. This will also happen if you do the same thing except the layers of stained glass are walls.

It doesn't always happen right away, sometimes you need to leave the area and come back for it to work. It seems like you can fix this by pressing F3 + A to reload the chunks, however the problem will reoccur if you leave the area and come back.

I did a few tests it seems like it most occurs when changing a resource pack. And it also seems to be sectioned off by the chunks? it also appears like sometimes you can only view this glitch from specific directions.