[BUG] Claude Haiku 3.5 hangs with MCP servers (works without MCP, Sonnet works with MCP)

Claude Code SDK Bug Report: Haiku 3.5 + MCP Server Incompatibility

Summary

Claude Haiku 3.5 (claude-3-5-haiku-20241022) hangs indefinitely during pre-flight check when used with MCP servers in Claude Code SDK. Sonnet 4.5 works correctly with identical configuration.

Environment

• Claude Code SDK Version: Latest (as of 2025-10-05)
• Python: 3.13
• OS: macOS Darwin 25.0.0
• Package Manager: uv

Issue Details

Expected Behavior

Agent should initialize MCP servers and execute within reasonable time (<2 min) when using Haiku 3.5, similar to Sonnet 4.5 performance.

Actual Behavior

Agent hangs indefinitely at "pre-flight check" stage with warning:

⚠️  [BashTool] Pre-flight check is taking longer than expected. Run with ANTHROPIC_LOG=debug to check for failed or slow API requests.

Reproduction Steps

1. Minimal Working Test (No MCP)

from claude_code_sdk import ClaudeCodeOptions, ClaudeSDKClient

options = ClaudeCodeOptions(
    model="claude-3-5-haiku-20241022",
    allowed_tools=[],
    mcp_servers={},
    system_prompt="You are a helpful assistant."
)

async with ClaudeSDKClient(options=options) as agent:
    await agent.query(prompt="Say 'Hello' in one word")
    async for msg in agent.receive_response():
        if hasattr(msg, 'result'):
            print(msg.result)

Result: ✅ Works perfectly (37 seconds)

2. Failing Test (With MCP Servers)

mcp_servers = {
    "github": {
        "command": "docker",
        "args": ["run", "-i", "--rm", "-e", "GITHUB_PERSONAL_ACCESS_TOKEN",
                 "ghcr.io/github/github-mcp-server"],
        "env": {"GITHUB_PERSONAL_ACCESS_TOKEN": os.getenv("GITHUB_TOKEN")}
    },
    "postgres": {
        "command": "npx",
        "args": ["-y", "mcp-postgres-full-access", os.getenv("DATABASE_URL")]
    }
}

options = ClaudeCodeOptions(
    model="claude-3-5-haiku-20241022",
    allowed_tools=["mcp__github", "mcp__postgres", "Bash", "Read"],
    mcp_servers=mcp_servers,
    system_prompt="You are an Issue Triage Bot."
)

async with ClaudeSDKClient(options=options) as agent:
    await agent.query(prompt="Analyze issue #1")
    async for msg in agent.receive_response():
        # Never reaches this point - hangs during pre-flight
        pass

Result: ❌ Hangs indefinitely (timeout after 5+ min)

3. Working Test (Sonnet with Same MCP Config)

Change only the model:

model="claude-sonnet-4-20250514"  # Instead of Haiku

Result: ✅ Works correctly (4-5 min execution)

Diagnostic Evidence

Test Results Summary

| Configuration | Model | MCP Servers | Time | Status |
|--------------|-------|-------------|------|--------|
| Minimal | Haiku 3.5 | None | 37 sec | ✅ Success |
| Full Agent | Haiku 3.5 | GitHub + PostgreSQL | Timeout | ❌ Hangs |
| Full Agent | Sonnet 4.5 | GitHub + PostgreSQL | 5 min | ✅ Success |

API Verification

Direct API calls to Anthropic work correctly:

curl https://api.anthropic.com/v1/messages \
  -H "x-api-key: $ANTHROPIC_API_KEY" \
  -H "anthropic-version: 2023-06-01" \
  -H "content-type: application/json" \
  -d '{"model": "claude-3-5-haiku-20241022", "max_tokens": 10, "messages": [{"role": "user", "content": "Hi"}]}'

Result: ✅ Returns response instantly

MCP Server Verification

Both MCP servers start correctly when tested independently:

• Docker GitHub MCP: ✅ Starts in <2 sec
• PostgreSQL MCP: ✅ Connects successfully

Zombie Process Detection

Found lingering MCP processes from failed Haiku attempts:

alex  55208  node .../mcp-postgres-full-access postgresql://...
alex  55192  npm exec mcp-postgres-full-access postgresql://...

These had to be manually killed (pkill -f mcp-postgres-full-access)

Hypothesis

Pre-flight check in Claude Code SDK has timing issues with faster models like Haiku 3.5. The SDK may:

1. Expect slower model response times for MCP initialization
2. Have race conditions when model responds faster than MCP servers initialize
3. Timeout logic incompatible with Haiku's speed characteristics

Impact

• ✅ Workaround exists: Use Sonnet 4.5 (slower but stable)
• ❌ Performance: Cannot leverage Haiku's 3-5x speed improvement with MCP
• ❌ Cost: Forced to use more expensive Sonnet model

Additional Context

MCP Servers Used

1. GitHub MCP: ghcr.io/github/github-mcp-server (Docker)
2. PostgreSQL MCP: mcp-postgres-full-access (npx)

Files for Reference

• Full agent code: [agent.py](./agent.py)
• Minimal test: [test_haiku.py](./test_haiku.py)

Expected Fix

SDK should handle fast model responses gracefully, regardless of MCP server initialization timing.

---

Reported by: Alex (Issue Triage Bot developer)
Date: 2025-10-05
Contact: GitHub @afoxnyc3