Quick answer: Have the autoload store data, not node references, and re-resolve scene nodes after each change; use is_instance_valid before touching any cached node.
change_scene_to_file frees the current scene before loading the next. Any global reference to a node in the old scene becomes invalid, and calling into it triggers a freed-instance error.
How to fix it
1. Store data in autoloads, not nodes
Keep plain data (scores, flags, the selected level) in the autoload. Let each scene pull what it needs on ready rather than the autoload holding live node references.
2. Validate before use
Wrap any cached node access in if is_instance_valid(node): so a freed reference is caught instead of crashing.
3. Re-resolve on scene ready
When the new scene's root enters the tree, have it register the nodes the global systems need, replacing the stale references from the previous scene.
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.
A crash you can name from its stack trace is a crash you can usually fix in minutes.