The name prototype is already used by WordPress.
In wp-includes/script-loader.php, you’ll find this line:
$scripts->add( 'prototype', 'https://ajax.googleapis.com/ajax/libs/prototype/1.7.1.0/prototype.js', array(), '1.7.1');
Your file will be correctly enqueued if you change the script handle:
wp_enqueue_script( 'yourprefix_prototype', plugins_url( '/prototype.js', __FILE__ ), array('jquery'), '1.0', true );
You’ll find the list of included JS scripts and their handles on the wp_enqueue_script() page.
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