The Sourcegraph security incident highlights the balance between using access tokens for efficient authentication and protecting them from malicious use. The hacker exploited a leaked access token to gain admin-level privileges, creating a proxy app that allowed unauthorized API usage. This incident emphasizes the importance of robust checks in automated build processes, secure token storage, and regular security audits. Best practices include short-lived access tokens, secure refresh tokens, encryption, secrets management, and implementing software composition analysis tools. The response to the breach is also crucial, with transparency about the discovery and details being vital for rebuilding trust with users.