Indeed, it’s not perfectly consistent. Even with everything else shut down, it can still fail.
Unfortunately we’re fighting a losing battle against modern JS build tooling here. It’s all designed to run on 8GB+ of Ram on modern developer machines, not 1GB VPSs 
We do have some solutions in mind. For example: providing pre-built assets which can be automatically downloaded. The big challenge we have is plugins, because they vary on everyone’s site, and right now they’re integrated tightly into the core build.
But for now, doing a full CLI rebuild should have a higher success rate than a web-ui update.