All my code runs twice when compiled by Webpack

in the template file you might have manually added a loading the bundle.

If you don't have the

inject: false 

option in

new HtmlWebpackPlugin({
    template: path.join(__dirname, '../src/index.html')
}),

the bundle will get added again.

Expanding a bit on @Emil Perhinschi's and @ggloren's earlier replies ...

Alternatively, if your ../src/index.html file does not rely on any script other than <script src="bundle.js"></script>, simply remove the latter from your index.html.

Per https://github.com/jantimon/html-webpack-plugin, the default for inject is true and ...

When passing true or 'body' all javascript resources will be placed at the bottom of the body element.

Thus your two instantiations of bundle.js are:

1. The <script src="bundle.js"></script> that you (presumably) coded, and
2. HtmlWebpackPlugin's injection "at the bottom of the body element".