Quick answer: Open the project in the editor and let the import finish (or run a headless import in CI), and never commit or hand-edit the .godot folder.
Every fresh clone of a Godot project must rebuild the import cache — the errors on first open are the cache being absent, not the repo being broken. Here is the correct handling everywhere it matters.
How to fix it
1. Let the first import complete
Open the project and wait for the import progress to finish before opening scenes; on big projects give it minutes, not seconds.
2. Import headlessly in CI
Run godot --headless --import (or an editor pass) as a pipeline step before exporting — exports from a cache-less checkout fail or ship broken assets.
3. Keep .godot ignored
Committing the cache seems to 'fix' clones but bloats the repo and desyncs across editor versions; the fix is regenerating, not versioning.
4. Commit the .import files though
Per-asset .import settings files must be in git — they carry compression and import options; only the generated .godot output is disposable.
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.