Quick answer: Find and revert unwanted overrides on instances so they inherit the prefab, or apply intended changes through the prefab, watching the override indicators.
Prefab overrides not applying is instance overrides winning. Reverting them fixes it. Here is how.
How to fix it
1. Revert unwanted overrides
An instance with an override on a property ignores the prefab's value for that property. If a prefab change is not reaching an instance, that property is likely overridden. Revert the override so it inherits again.
2. Watch the override indicators
Overridden properties are marked (bold, with a blue line) on the instance. Use these indicators to see what is overridden, so you know why a prefab change is not propagating to a particular instance.
3. Apply changes through the prefab
To change all instances, edit the prefab itself (in prefab mode) for non-overridden properties. For overridden ones, either revert the overrides or apply the instance's value to the prefab deliberately.
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.
A crash you can name from its stack trace is a crash you can usually fix in minutes.