index.js

const dm = require('deepmerge');

if (typeof dm !== 'function') {
    throw new Error("require('deepmerge') is not a function");
}

index.mjs

import dm from 'deepmerge';

if (typeof dm !== 'function') {
    throw new Error("require('deepmerge') is not a function");
}

package.json

{
  "name": "webpack-cjs-issue",
  "version": "1.0.0",
  "main": "index.js",
  "license": "MIT",
  "dependencies": {
    "deepmerge": "^2.1.0",
    "webpack": "^4.5.0"
  },
  "devDependencies": {
    "webpack-cli": "^2.0.14"
  },
  "scripts": {
    "test-webpack": "webpack && node dist/bundle.js",
    "test-node-cjs": "node index.js",
    "test-node-esm": "node --experimental-modules index.mjs"
  }
}

webpack.config.js

module.exports = {
  entry: './index.js',
  output: {
    filename: 'bundle.js'
  }
};