Why is my JQuery selector returning a n.fn.init[0], and what is it?

Another approach(Inside of $function to asure that the each is executed on document ready):

var ids = [1,2];
$(function(){
  $('.checkbox-wrapper>input[type="checkbox"]').each(function(i,item){
    if(ids.indexOf($(item).data('id')) > -1){
       $(item).prop("checked", "checked");
    }
  });
});

Working fiddle: https://jsfiddle.net/robertrozas/w5uda72v/

What is the n.fn.init[0], and why it is returned? Why are my two seemingly identical JQuery functions returning different things?

Answer: It seems that your elements are not in the DOM yet, when you are trying to find them. As @Rory McCrossan pointed out, the length:0 means that it doesn’t find any element based on your search criteria.

About n.fn.init[0], lets look at the core of the Jquery Library:

var jQuery = function( selector, context ) {
   return new jQuery.fn.init( selector, context );
};

Looks familiar, right?, now in a minified version of jquery, this should looks like:

var n = function( selector, context ) {
   return new n.fn.init( selector, context );
};

So when you use a selector you are creating an instance of the jquery function; when found an element based on the selector criteria it returns the matched elements; when the criteria does not match anything it returns the prototype object of the function.