Install as mu-plugin to get dump of all hooks invoked more than once.

hook-count.php

<?php
/**
 * Plugin Name: Hook Counter
 * Author: Weston Ruter
 * Description: Drop in mu-plugins and see a markdown table at the end of a page's source code counting all hooks invoked more than once.
 */

$hook_counts = [];

add_filter( 'all', static function ( $hook_name ) use ( &$hook_counts ) {
	if ( ! isset( $hook_counts[ $hook_name ] ) ) {
		$hook_counts[ $hook_name ] = 1;
	} else {
		$hook_counts[ $hook_name ]++;
	}
}, PHP_INT_MIN );

add_action( 'shutdown', static function () use ( &$hook_counts ) {
	arsort( $hook_counts );
	echo "\n<!--\n";
	echo "Hook | Count\n";
	echo "-- | --:\n";
	foreach ( $hook_counts as $hook_name => $hook_count ) {
		if ( $hook_count > 1 ) {
			printf( "%s | %s\n", $hook_name, number_format( $hook_count ) );
		}
	}
	echo "-->\n";
}, PHP_INT_MAX );