Dark prismarine in the new default textures has an improper outline that makes the "tiles" appear to be 3 by 3 instead of 2 by 2 (not counting the visible outline), causing weird interactions with other blocks that make dark prismarine look like it is sticking to other blocks on certain sides. This problem is also apparent when looking at prismarine stairs facing a certain direction. The programmer art texture pack does not have this problem, as shown in the screenshots.
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I don't really see what's the issue here – to me, both textures look basically the same, except the new one has different colors.
In the programmer art texture pack, there are brighter pixels to contrast with the dark grid and make the center of the tiles 2 by 2, but the brighter outline is missing in the new textures. For every 16 pixels forming a "tile", there are 7 darker pixels, 5 lighter pixels, and 4 normal pixels; the said lighter pixels are non existent or not emphasized enough to be seen as a proper outline.
This problem used to happen with quartz blocks (MC-146080), as well the polished variants of andesite, diorite, and granite when the new textures were in progress.
gaspoweredpick
Programmer art tiles are also 3x3. I think you're referring to some sort of texture offset.