WP_Query, a comma-separated list of term slugs works fine:
$query = new WP_Query ( array( 'customtaxonomy' => 'term1,term2' ) );
...but an array of slugs causes a warning:
$query = new WP_Query ( array( 'customtaxonomy' => array( 'term1', 'term2' ) ) );
Warning: urlencode() expects parameter 1 to be string, array given in /path/to/wp-includes/formatting.php on line 3253
Another WPSE post proposes that this could be WP looking for hierarchy in a hierarchical taxonomy, but I can't think of any way to make sense of this behaviour. Do you know why this is happening?