[BUG] Making tool calls to Atlassian MCP with tool search enabled results in a 500

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?

I advised folks to turn off tool search if they plan to use Atlassian MCP (ENABLE_TOOL_SEARCH = false), since Claude Code 2.1 does not work with Atlassian MCP if tool search is enabled. You’ll get a 500 error:

Use Atlassian MCP
 ⎿ 500 messages.2.content.0.tool_result.content.0: Input tag 'tool_reference' found
   using 'type' does not match any of the expected tags: 'document', 'image',
   'search_result', 'text'

This worked in 2.0.33 and 2.0.72, started failing in 2.1.

What Should Happen?

Claude code with tool search enabled should allow tool interactions with Atlassian MCP

Error Messages/Logs

500 messages.2.content.0.tool_result.content.0: Input tag 'tool_reference' found
   using 'type' does not match any of the expected tags: 'document', 'image',
   'search_result', 'text'

Steps to Reproduce

1. Make sure ENABLE_TOOL_SEARCH is not set to false
2. Connect to Atlassian MCP https://github.com/sooperset/mcp-atlassian
3. Try to get a Jira issue

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.0.72

Claude Code Version

2.1.34

Platform

AWS Bedrock

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_