[BUG] Agent SDK MCP tools intermittently fail to execute - CLI not sending control_request

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When using SDK MCP servers (create_sdk_mcp_server with @tool decorator), tool calls intermittently fail to execute. The agent generates valid tool calls, but the Python tool handlers never run.

What Should Happen?

When the agent produces a tool block it should trigger the MCP to execute the tool and continue.

Error Messages/Logs

Steps to Reproduce

mcp_bug_issue.md

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.12 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_