Quick answer: Register the manager only once as an autoload and never also place it in a scene tree; if you need a single guaranteed instance, guard against duplicates in _enter_tree.
Godot autoloads are added under the root automatically. Dropping the same scene into a level creates a second instance, so signals fire twice and global state diverges.
How to fix it
1. Pick one ownership model
Either register the manager as an autoload in Project Settings > Autoload, or instance it in a scene, never both. Autoload is the right choice for a game-scoped singleton.
2. Reference it by its global name
Access the autoload through its registered name (for example GameState) from any script instead of instancing the scene that defines it.
3. Guard against accidental duplicates
In _enter_tree, if a static reference is already set, call queue_free() on the extra instance so only the first survives.
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 Godot 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.