Cursor starts duplicate GitHub MCP server instances

[Damith88]

Bug Description

Cursor consistently starts 2 instances of the GitHub MCP server when it should only start 1. This results in duplicate Docker containers running the ghcr.io/github/github-mcp-server image.

Expected Behavior

Cursor should start exactly 1 GitHub MCP server instance as configured in ~/.cursor/mcp.json.

Actual Behavior

Cursor starts 2 GitHub MCP server Docker containers, leading to:

• Duplicate resource usage
• Potential confusion about which instance is active
• Unnecessary Docker containers running

Steps to Reproduce

1. Configure GitHub MCP in ~/.cursor/mcp.json with a single github entry:

{
  "mcpServers": {
    "github": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm",
        "-e", "GITHUB_PERSONAL_ACCESS_TOKEN",
        "ghcr.io/github/github-mcp-server"
      ],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "${env:GITHUB_PERSONAL_ACCESS_TOKEN}"
      }
    }
  }
}

2. Start Cursor
3. Check running Docker containers: docker ps | grep github-mcp-server
4. Observe 2 containers running instead of 1

Environment

• OS: macOS (darwin 24.6.0)
• Cursor: Latest version
• MCP Configuration: Single GitHub MCP server entry in ~/.cursor/mcp.json
• Docker: Running

Additional Context

• This occurs consistently, not intermittently
• Codex (if running) correctly starts only 1 instance
• The issue persists across Cursor restarts
• Only 1 Cursor window/workspace is open
• The --rm flag should auto-remove containers, but they remain running until manually stopped

Related

Related to issue #3675

[zestysoft]

This isn't limited to github mcp server unfortunately. I've loaded the mitre-attack mcp server via docker and see 4 instances running in docker. These also remain running even after cursor is terminated.