A simple script that check if exist some conflict with all Resources folders in project. For use it just go to ' Window/ResourcesCheckConflict '

ResourcesCheckConflict.cs

//This script put inside a Folder with the name 'Editor'

//Developer by ARKMs , use it with total liberty

using UnityEngine;
using UnityEditor;
using System;
using System.IO;
using System.Collections.Generic;

public class ResourcesCheckConflict
{ 

	[MenuItem( "Window/ResourcesCheckConflict" )]
	static void ResourcesCheckConflictCall()
	{
		CheckResourcesConflict();
	}

	class RESOURCESDATA
	{
		public string name;
		public string path;

		public RESOURCESDATA( string path )
		{
			string fullAssetsPath = Path.GetFullPath("Assets").Replace('\\', '/');
			path = path.Replace('\\', '/');
			path = path.Replace(fullAssetsPath, "");

			this.path = path;
			var parts = path.Split( new string[] { "Resources/" }, StringSplitOptions.RemoveEmptyEntries );
			this.name = parts[1];
		}
	}

	static void CheckResourcesConflict()
	{	
		// find all Resources folders
		string[] dirs = Directory.GetDirectories( Application.dataPath, "Resources", SearchOption.AllDirectories );
		List<RESOURCESDATA> resources = new List<RESOURCESDATA>();

        //Get all files
		for(int i=0; i<dirs.Length; i++)
		{
			resources.AddRange( getAllResourcesAtPath( dirs[i] ) );
		}

        //Check if exist a conflict
		List<string> resourceNames = new List<string>();
        List<string> resourcePath = new List<string>(); //This only helps show the path in conflict
        for (int i=0; i<resources.Count; i++)
		{
			if(resourceNames.Contains( resources[i].name ) )
			{
				Debug.LogError ( "Conflict: " + resources[i].name + " path " + resources[i].path + "  with: " + resourcePath[resourceNames.IndexOf(resources[i].name)]);
				continue;
			}
            resourceNames.Add( resources[i].name );
            resourcePath.Add(resources[i].path);
        }

		Debug.Log ("--finish check Resources conflict--");
	}

    //This function return all files inside a Resources folder
	static List<RESOURCESDATA> getAllResourcesAtPath( string path )
	{
		List<RESOURCESDATA> resources = new List<RESOURCESDATA>();

		string[] files = Directory.GetFiles( path, "*", SearchOption.AllDirectories );
		for(int i=0; i<files.Length; i++)
		{
			if( files[i].EndsWith( ".meta" ) || files[i].EndsWith( ".db" ) || files[i].EndsWith( ".DS_Store" ) )
				continue;

			resources.Add( new RESOURCESDATA(files[i]) );
		}

		return resources;
	}
}