Quick answer: Call Undo.RecordObject on the exact target immediately before you modify it, mark it dirty afterward, and use Undo.RegisterCreatedObjectUndo or RegisterFullObjectHierarchyUndo for structural changes.
Your custom tool changes a component, but pressing Ctrl+Z does nothing or only partly reverts. The undo system records the object's state at the moment you call RecordObject, so timing and target identity are everything.
How to fix it
1. Record before you mutate
Call Undo.RecordObject(target, "My Change") immediately before changing any field. Recording after the change captures the new state, so undo has nothing to roll back to.
2. Record every affected object
If you touch several components or children, record each one, or use Undo.RegisterFullObjectHierarchyUndo for a whole GameObject tree so the entire change is reversible in one step.
3. Mark dirty and handle creation
After editing, call EditorUtility.SetDirty(target) so the change persists, and use Undo.RegisterCreatedObjectUndo when you instantiate objects so undo can delete them.
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.