Minecraft does not process some PNGs correctly. Specifically, it does not seem to implement the tRNS specification fully, nor does it handle greyscale PNGs correctly. Attached are some vanilla textures from the most recent snapshot as of this writing (15w42a) that render incorrectly when compressed with ScriptPNG's most aggressive lossless setting. (If Mojang did this compression themselves, Minecraft's PNGs would be 34.45% [1299 KB] smaller, which is a not-insignificant amount of bandwidth.)