Quick answer: Tag the pass with Queue=Transparent and RenderType=Transparent, set ZWrite Off and proper blend modes, and rely on per-object distance sorting for correct order.
Custom transparency breaks sorting when it inherits opaque queue defaults or writes to the depth buffer. Unity sorts transparent objects by camera distance only when they are in the Transparent queue with depth writes off. Here is how to fix it.
How to fix it
1. Set the transparent queue tags
Add Tags { "Queue"="Transparent" "RenderType"="Transparent" } so the object is drawn after opaques and sorted back-to-front by distance.
2. Disable depth writes
Set ZWrite Off and a standard alpha blend such as Blend SrcAlpha OneMinusSrcAlpha; writing depth on a transparent surface causes it to occlude objects behind it incorrectly.
3. Fix intra-object sorting separately
Per-object distance sorting cannot order overlapping triangles within one mesh; for that, split the mesh, use a two-pass ZWrite-then-color approach, or accept the limitation for convex shapes.
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.
Ship the fix, watch the signature disappear from the next build. That's how you know it's really gone.