Quick answer: Use the built-in interactive Handles (PositionHandle, FreeMoveHandle) which manage their own control IDs, and for custom hit testing call Handles.Button or consume the event with Event.current.Use().
You draw helper handles in OnSceneGUI, but clicking them does nothing or just rotates the camera. The scene view is grabbing the mouse because your handles never claim it.
How to fix it
1. Use interactive handle APIs
Prefer Handles.PositionHandle, Handles.FreeMoveHandle, or Handles.Button. These allocate control IDs and report drag deltas, so the scene view yields input to them.
2. Consume the event
When you handle a click yourself, call Event.current.Use() so the event does not fall through to the scene view's camera navigation.
3. Record undo on change
Wrap handle interactions in EditorGUI.BeginChangeCheck() / EndChangeCheck() and call Undo.RecordObject when a change is detected so the manipulation is undoable.
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.