Error: Duplicate plugin/preset detected when updating babel from 6.22 to 7.4 for react app

[Tianpei9]

Bug Report

Current Behavior
A clear and concise description of the behavior.
Use npx babel-upgrade --write to update babel, but get this duplication issue, I check them but can't find which plugin or preset is duplicated
Input Code

• REPL or Repo link if applicable:
  This is new .bablerc file

{
    "presets": [
        "@babel/preset-react",
        "@babel/preset-env",
        "@babel/env"
    ],
    "plugins": [
        ["@babel/plugin-proposal-object-rest-spread", {}, "unique-name-a"],
        ["@babel/plugin-syntax-dynamic-import", {}, "unique-name-b"],
        ["@babel/plugin-syntax-import-meta", {}, "unique-name-d"],
        ["@babel/plugin-proposal-class-properties", {}, "unique-name-c"],
        ["@babel/plugin-proposal-json-strings", {}, "unique-name-e"],
        [
            ["@babel/plugin-proposal-decorators", {}, "unique-name-p"],
            {
                "legacy": true
            }
        ],
        ["@babel/plugin-proposal-function-sent", {}, "unique-name-f"],
        ["@babel/plugin-proposal-export-namespace-from", {}, "unique-name-g"],
        ["@babel/plugin-proposal-numeric-separator", {}, "unique-name-h"],
        ["@babel/plugin-proposal-throw-expressions", {}, "unique-name-i"],
        ["@babel/plugin-proposal-export-default-from", {}, "unique-name-j"],
        ["@babel/plugin-proposal-logical-assignment-operators", {}, "unique-name-k"],
        ["@babel/plugin-proposal-optional-chaining", {}, "unique-name-l"],
        [
            ["@babel/plugin-proposal-pipeline-operator", {}, "unique-name-q"],
            {
                "proposal": "minimal"
            }
        ],
        ["@babel/plugin-proposal-nullish-coalescing-operator", {}, "unique-name-m"],
        ["@babel/plugin-proposal-do-expressions", {}, "unique-name-n"],
        ["@babel/plugin-proposal-function-bind", {}, "unique-name-o"],
    ]
}

webpack.config.js file: (didn't do any change)

const webpack = require('webpack')
const ExtractTextPlugin = require('extract-text-webpack-plugin')
const path = require('path')

module.exports = {
  devtool: 'source-map',
  entry: [
    'babel-polyfill',
    './public/scripts/main',
  ],
  module: {
    loaders: [
      {test: /.json$/, loader: 'json'},
      {test: /\.hbs$/, loader: 'handlebars'},
      {test: /.jsx?$/, loader: 'babel', exclude: /node_modules\/(?!ol)/},
    ],
  },
  output: {
    filename: 'bundle.js',
    path: `${__dirname}/public/scripts/`,
  },
  plugins: [
    new webpack.DefinePlugin({
      'process.env': {
        NODE_ENV: '"production"',
      },
    }),
    new webpack.IgnorePlugin(/regenerator|nodent|js-beautify/, /ajv/),
    new webpack.optimize.OccurenceOrderPlugin(),
    new webpack.optimize.DedupePlugin(),
    new webpack.optimize.UglifyJsPlugin({
      compress: {
        warnings: false,
      },
      dead_code: true,
      minimize: true,
    }),
  ],
  resolve: {
    extensions: [
      '',
      '.js',
      '.json',
      '.jsx',
    ],
    alias: {
      'ol': path.resolve(__dirname, './', 'node_modules/ol'),
      'react': path.resolve(__dirname, './', 'node_modules/react'),
      'react-dom': path.resolve(__dirname, './', 'node_modules/react-dom'),
      'styled-components': path.resolve(__dirname, './', 'node_modules/styled-components')
    }
  },
}

Expected behavior/code
A clear and concise description of what you expected to happen (or code).

Babel Configuration (.babelrc, package.json, cli command)

Environment

• Babel version(s): 7.00
• Node/npm version: Node 8/npm 5]
• OS: OSX 10.13.4
• Monorepo: [e.g. yes/no/Lerna]
• How you are using Babel: loader

Possible Solution

Additional context/Screenshots
Add any other context about the problem here. If applicable, add screenshots to help explain.

[babel-bot]

Hey @Tianpei9! We really appreciate you taking the time to report an issue. The collaborators
on this project attempt to help as many people as possible, but we're a limited number of volunteers,
so it's possible this won't be addressed swiftly.

If you need any help, or just have general Babel or JavaScript questions, we have a vibrant Slack
community that typically always has someone willing to help. You can sign-up here
for an invite.

[loganfsmyth]

You do have the same thing.

        "@babel/preset-env",
        "@babel/env"

is the same preset listed twice, one just includes the preset- prefix and one doesn't.