Quick answer: Give each pickup a stable unique ID, record collected IDs in a persistent autoload, and on room ready free any pickup whose ID is already in the collected set.
Backtracking is core to metroidvanias, so a re-entered room must remember what you took. The fix is to store collected IDs globally and skip spawning them when the room loads again.
How to fix it
1. Give each pickup a stable ID
Assign every gem a unique identifier such as roomname_gem_03 that does not change between sessions. A position-based or auto-generated ID will break the moment you edit the scene.
2. Track collected IDs in an autoload
On pickup, call GameState.collected.append(id) in a singleton that persists across room changes. This set is your authority for what no longer exists in the world.
3. Filter on room ready
In the room's _ready(), loop its pickups and queue_free() any whose ID is already in GameState.collected. The player sees only gems they have not yet taken.
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.