webpack minify HtmlWebpackPlugin

Not sure what is the issue you are facing exactly, but you can try passing explicit parameters in your minify property instead of a boolean. For example, to remove whitespace try the following:

Try:

new HtmlWebpackPlugin({
    template: './src/ejs/index.ejs',
    filename: 'index.ejs',
    minify: {
        collapseWhitespace: true
    }
})

This works for me.

For the full list of options check the documentation.