What Are the Critical MCP Security Risks Every Developer Must Know?

Jul 24, 2025

5 mins

Matt (Co-Founder and CEO)

Nothing is more frustrating than an MCP server that works perfectly in development but fails mysteriously in production. Whether you're facing connection timeouts, protocol errors, or silent failures, debugging MCP servers requires a systematic approach and the right tools.

This comprehensive guide covers the most common MCP server issues encountered in production environments and provides practical solutions to get your servers running smoothly.

Understanding MCP Error Categories

MCP server issues generally fall into five main categories, each requiring different debugging strategies:

1. Connection and Transport Issues

These are the most common problems, often manifesting as:

"Connection refused" errors
Timeouts during server initialization
Intermittent disconnections
Protocol handshake failures

2. Protocol Compliance Problems

JSON-RPC protocol violations that cause:

Message parsing errors
Invalid response formats
Missing required fields
Version compatibility issues

3. Tool Execution Failures

Runtime errors in your MCP tools:

Unhandled exceptions in tool functions
Invalid parameter validation
External API failures
Resource access problems

4. Performance and Resource Issues

Problems that affect server reliability:

Memory leaks and high CPU usage
Slow response times
Resource exhaustion
Deadlocks and race conditions

5. Authentication and Authorization Failures

Security-related issues:

Token validation errors
Permission denied responses
Session management problems
OAuth flow failures

Essential Debugging Tools

MCP Inspector: Your Primary Debugging Tool

The MCP Inspector is an invaluable tool for testing and debugging MCP servers. Install and use it to test your server directly:

# Install the MCP Inspector
npm install -g @modelcontextprotocol/inspector

# Test your local MCP server
npx @modelcontextprotocol/inspector path/to/your/mcp-server

# Test with custom port
CLIENT_PORT=8080 SERVER_PORT=9000

The Inspector provides a web interface where you can:

View real-time protocol messages
Test individual tools and resources
Inspect server capabilities
Monitor connection status

Setting Up Comprehensive Logging

Proper logging is crucial for debugging MCP servers. Here's a production-ready logging setup:

// logger.js
const winston = require('winston');

const logger = winston.createLogger({
  level: process.env.LOG_LEVEL || 'info',
  format: winston.format.combine(
    winston.format.timestamp(),
    winston.format.errors({ stack: true }),
    winston.format.json()
  ),
  defaultMeta: { service: 'mcp-server' },
  transports: [
    new winston.transports.File({ filename: 'error.log', level: 'error' }),
    new winston.transports.File({ filename: 'combined.log' }),
    new winston.transports.Console({
      format: winston.format.simple()
    })
  ]
});

// Add correlation IDs for request tracking
const addCorrelationId = (req, res, next) => {
  req.correlationId = require('uuid').v4();
  logger.defaultMeta.correlationId = req.correlationId;
  next();
};

module.exports = { logger, addCorrelationId };

Network Debugging Tools

Use these command-line tools to diagnose network-related issues:

# Check if your MCP server is listening on the expected port
netstat -tlnp | grep :3000

# Test connectivity to your server
telnet localhost 3000

# Monitor network traffic
tcpdump -i any -n port 3000

# Test HTTP endpoints
curl -v

Debugging Connection Issues

Problem: "Connection Refused" Errors

This is typically the first error you'll encounter. Here's a systematic approach to diagnose it:

Step 1: Verify Server Process

# Check if your server process is running
ps aux | grep mcp-server

# Check server logs for startup errors
tail -f /var/log/mcp-server.log

# Verify the server is binding to the correct interface
ss -tlnp | grep

Step 2: Validate Configuration

// debug-config.js - Add this to your server startup
console.log('Server Configuration:', {
  port: process.env.PORT || 3000,
  host: process.env.HOST || '0.0.0.0',
  nodeEnv: process.env.NODE_ENV,
  databaseUrl: process.env.DATABASE_URL ? 'configured' : 'missing'
});

// Validate required environment variables
const requiredEnvVars = ['DATABASE_URL', 'MCP_API_KEY'];
const missingVars = requiredEnvVars.filter(varName => !process.env[varName]);

if (missingVars.length > 0) {
  console.error('Missing required environment variables:', missingVars);
  process.exit(1);
}

Step 3: Test with Minimal Server Create a minimal test server to isolate the problem:

// minimal-test-server.js
const http = require('http');

const server = http.createServer((req, res) => {
  res.writeHead(200, { 'Content-Type': 'application/json' });
  res.end(JSON.stringify({ status: 'ok', timestamp: new Date().toISOString() }));
});

server.listen(3000, '0.0.0.0', () => {
  console.log('Minimal test server running on port 3000');
});

server.on('error', (error) => {
  console.error('Server error:', error);
});

Problem: Intermittent Connection Drops

Intermittent connection issues are harder to debug but often relate to resource exhaustion or network instability:

// connection-monitor.js
const EventEmitter = require('events');

class ConnectionMonitor extends EventEmitter {
  constructor(server) {
    super();
    this.server = server;
    this.connections = new Set();
    this.setupMonitoring();
  }

  setupMonitoring() {
    this.server.on('connection', (socket) => {
      this.connections.add(socket);
      console.log(`New connection: ${socket.remoteAddress}:${socket.remotePort}`);
      console.log(`Total connections: ${this.connections.size}`);

      socket.on('close', () => {
        this.connections.delete(socket);
        console.log(`Connection closed. Remaining: ${this.connections.size}`);
      });

      socket.on('error', (error) => {
        console.error('Socket error:', error);
        this.connections.delete(socket);
      });
    });

    // Monitor connection health every 30 seconds
    setInterval(() => {
      console.log(`Health check: ${this.connections.size} active connections`);
      this.checkResourceUsage();
    }, 30000);
  }

  checkResourceUsage() {
    const memUsage = process.memoryUsage();
    console.log('Memory usage:', {
      rss: `${Math.round(memUsage.rss / 1024 / 1024)} MB`,
      heapUsed: `${Math.round(memUsage.heapUsed / 1024 / 1024)} MB`,
      external: `${Math.round(memUsage.external / 1024 / 1024)} MB`
    });

    // Alert if memory usage is high
    if (memUsage.heapUsed > 500 * 1024 * 1024) { // 500MB
      console.warn('High memory usage detected');
      this.emit('highMemoryUsage', memUsage);
    }
  }
}

// Usage
const monitor = new ConnectionMonitor(server);
monitor.on('highMemoryUsage', (usage) => {
  // Implement alerting or graceful degradation
  console.error('Memory usage alert:', usage);
});

Debugging Protocol Issues

Problem: JSON-RPC Parsing Errors

MCP uses JSON-RPC 2.0, and protocol violations will cause immediate failures:

// protocol-validator.js
function validateJSONRPC(message) {
  const errors = [];

  // Check required fields
  if (!message.jsonrpc || message.jsonrpc !== '2.0') {
    errors.push('Missing or invalid jsonrpc version');
  }

  if (!message.method && !message.result && !message.error) {
    errors.push('Message must have method, result, or error');
  }

  if (message.method && typeof message.method !== 'string') {
    errors.push('Method must be a string');
  }

  if (message.id !== undefined && typeof message.id !== 'string' && typeof message.id !== 'number') {
    errors.push('ID must be string, number, or null');
  }

  return errors;
}

// Middleware to validate all incoming messages
function validateIncomingMessage(req, res, next) {
  try {
    const message = JSON.parse(req.body);
    const errors = validateJSONRPC(message);
    
    if (errors.length > 0) {
      console.error('Protocol validation failed:', errors);
      res.status(400).json({
        jsonrpc: '2.0',
        error: {
          code: -32600,
          message: 'Invalid Request',
          data: errors
        },
        id: message.id || null
      });
      return;
    }
    
    req.jsonrpc = message;
    next();
  } catch (error) {
    console.error('JSON parsing error:', error);
    res.status(400).json({
      jsonrpc: '2.0',
      error: {
        code: -32700,
        message: 'Parse error'
      },
      id: null
    });
  }
}

Problem: stdout/stderr Confusion

A critical rule for MCP servers: only JSON-RPC messages should go to stdout, everything else to stderr:

// stdout-manager.js
class StdoutManager {
  constructor() {
    this.originalConsoleLog = console.log;
    this.originalConsoleError = console.error;
    this.setupRedirection();
  }

  setupRedirection() {
    // Redirect console.log to stderr to avoid protocol interference
    console.log = (...args) => {
      process.stderr.write(`[LOG] ${args.join(' ')}\n`);
    };

    console.error = (...args) => {
      process.stderr.write(`[ERROR] ${args.join(' ')}\n`);
    };
  }

  writeJSONRPC(message) {
    // Only JSON-RPC messages should go to stdout
    process.stdout.write(JSON.stringify(message) + '\n');
  }

  restore() {
    console.log = this.originalConsoleLog;
    console.error = this.originalConsoleError;
  }
}

// Usage
const stdoutManager = new StdoutManager();

// Send JSON-RPC response
stdoutManager.writeJSONRPC({
  jsonrpc: '2.0',
  result: { status: 'success' },
  id: 1
});

Debugging Tool Execution Issues

Problem: Tool Functions Throwing Unhandled Exceptions

Wrap all tool functions with comprehensive error handling:

// tool-wrapper.js
function createSafeTool(toolName, toolFunction) {
  return async function safeTool(params) {
    const startTime = Date.now();
    const correlationId = require('uuid').v4();
    
    try {
      console.error(`[${correlationId}] Starting tool: ${toolName}`, { params });
      
      // Validate parameters
      if (!params || typeof params !== 'object') {
        throw new Error('Invalid parameters: expected object');
      }

      const result = await toolFunction(params);
      
      console.error(`[${correlationId}] Tool completed: ${toolName} in ${Date.now() - startTime}ms`);
      return result;
      
    } catch (error) {
      console.error

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