This is only noticeable when using a model that does not specify uv coordinates. That is, one that uses the game's default parametric projections (NOT uv-lock). This is also NOT a model error.
Summary:
Projections on the north, east, and down faces are taken from the south, west, and up faces; they are not taken independently. In 1.9 snapshots the errors form on the east and west faces instead.
Details:
The spruce door in the screenshot uses the custom model (argon_door_generic) attached to this report. The front of the door is the west face and the side of the door is the north face. The north face (side) does not specify uv coords, so the texture should be taken from a projection, logically [13,0,16,16]. Instead, the face uses the coords [0,0,3,16].
As you can also see in the fences, the faces are using the same uv for opposite faces which are in different positions.
Lastly, the altered cube.json splits the cube model into eight small cubes, showing the exact error in the projection. The uv for the north, east, and down faces is the same as the uv for the south, west, and up faces.
The bug affects the north, east, and down faces (east and west faces in 1.9). This is the same bug as MC-45375 , MC-2053 , and MC-190 . This also relates to MC-37106 , the result of (improperly) fixing the bug.
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Affects 1.8 pre-1!

Am I correct in assuming that the game only does projections for three of the faces and then infers (incorrectly) the texture uv for the other three?

The result of altering the cube model into eight smaller cubes.

I guess that all these errors are caused by impropper modeling

It's actually the game going "Let's see...I'll take the uv for the south face, phase it through the block to the north face, then flip the texture!"

Is this going to be reassigned?

Confirmed for 15w31 (a-c)?
I changed my beacon model to have a full-sized obsidian bottom, pushing the glass up. On the east and west side, projections are taken from [ 0, 3, 16, 16 ] instead of [ 0, 0, 16, 13 ] (in other words, the texture is offset, making it look upside-down [because the top of the texture is cut off instead of the bottom] on the east/west compared to the other sides)

I believe i'm seeing this same error. Custom models that worked fine in 1.8 (which doesn't specify all UV coordinates) have textures that have aligned differently in the snapshot.

Still exists in 15w32c, but it affects the east and west faces instead, vertically. This affects item models too. It needs to be fixed as soon as possible.

This bug completely defeats the purpose of using UV projections! It needs to be fixed the rest of the way for 1.9.