Using custom taxonomies in a query

I looked at the source code for IssueM. I think the slug you are after is issuem_issue

However, there are two more taxonomies it registers: issuem_issue_categories and issuem_issue_tags

Edit

Try changing your args to:

$args = array(
    'post_type' => 'article',
    'tax_query' => array(
         array(
           'taxonomy' => 'issuem_issue',
           'field'    => 'slug',
           'terms'    => 'issue-one'
     ),
 ),
 'posts_per_page' => -1
 );

This should all articles with the issuem_issue taxonomy slugged ‘issue-one’ attached to it.