I recently spent a bit of time trying to determine how to get the categories of a custom post type, I though that it would be very easy and if I had known the function below it probably would have done.

I was extending a testimonials widget and wanted to filter the testimonials by a selected category, so whilst in the loop I wanted to see if this product was associated to a predefined category within the custom post type (testimonials in this case). Below shows you how I did it, the function that you need to find this is wp_get_post_terms()

//$test_n_cat is the category we are looking to match
//$showEnt is whether to show this entry in the loop
$showEnt = true;
     if($test_n_cat) {
      $term_list = wp_get_post_terms(get_the_ID(), 'category-testimonial', 
      array("fields" => "all"));
      $showEnt = false;
      //check to see what cat the post is in
      foreach($term_list as $t){
       if($t->term_id == $test_n_cat){
        $showEnt = true;
        //now show the testimonial

Here $test_n_cat is the category that I am looking to match. There maybe other ways to achieve this but this is working well for me, I hope this helps.