Quick answer: Add UNITY_VERTEX_INPUT_INSTANCE_ID, UNITY_SETUP_INSTANCE_ID and stereo eye index macros to the shader so it picks the correct per-eye view-projection.
Single-pass instanced rendering draws both eyes in one pass using GPU instancing, which is the fast path for VR. A custom shader that ignores the stereo instancing macros renders with one eye's matrices, so the effect appears in the left eye and is missing or misaligned in the right.
How to fix it
1. Declare the instance ID
Add UNITY_VERTEX_INPUT_INSTANCE_ID to your appdata and varyings structs so the eye index travels through the shader.
2. Set up stereo in the vertex stage
Call UNITY_SETUP_INSTANCE_ID(v) and UNITY_INITIALIZE_VERTEX_OUTPUT_STEREO(o) at the top of the vertex function before transforming positions.
3. Resolve eye in the fragment stage
Call UNITY_SETUP_STEREO_EYE_INDEX_POST_VERTEX(i) in the fragment shader so per-eye textures and matrices sample the right eye.
Catching the ones you can't reproduce
The hardest version of this to fix is the one you can't reproduce — it only happens on a player's hardware, OS, driver, or save state, under conditions that simply aren't present on your machine. A report that says “it crashed” or “it froze” gives you nothing to act on, so the bug survives release after release while quietly costing you players.
Automatic error capture closes that gap. Each failure arrives with its full stack trace, the device and OS, the build number, and a breadcrumb trail of what the player did right before it broke, so even a failure you have never seen becomes a specific, reproducible issue. Fold identical failures into one signature ranked by how many players each hits, and your worklist sorts itself worst-first instead of arriving as a stream of vague complaints.
This is where a tool like Bugnet earns its place. Its SDK captures every Unity error automatically with the full stack trace plus device, OS, memory, build, and game-state context, folds duplicates into one grouped issue with an occurrence count, and ties each to the build it first appeared on — so you fix the problem that hurts the most players first and confirm it is gone when its signature disappears from the next release.
Most of the time the fix is small. Seeing the failure clearly is the part that actually costs you.