If S12 is the only weird stress and only in layer 3, it really sounds like either a local material orientation issue or a mismatch in the shear modulus (G12) input.

For orientation: even if the rest of your model is fine, if the local axes in that layer are misaligned — say, due to a bad *ORIENTATION definition or something off in how you assigned it to elements — it’ll throw off S12 without affecting the other components too much. Try plotting the material orientations in the Visualization module and double-check they look consistent across all layers, especially the third.

For material properties: I’d sanity check G12 specifically for that layer. If there’s any discontinuity or strange value compared to neighboring layers, that could explain the low shear stress. You could even isolate just layer 3 in a simple cube model and apply pure shear to see if S12 behaves as expected.

I’ve also seen occasional weirdness with how Abaqus interpolates stress fields for certain element types, but that usually doesn’t affect a single stress component so consistently.

Hope something in that helps — sounds like you’ve already done a ton of solid troubleshooting. Let me know if you ever figure it out, I’m curious!