Filters are for modifying data that's passed through them. You need to take the input, modify it, then return
it.
function exclude_not_allowed_terms( $args, $taxonomies ) {
if(!current_user_can('edit_others_posts')
&& in_array( 'my-taxonomy', $taxonomies ) ) {
$args['meta_query'] = array(
array(
'key' => 'owner',
'value' => get_current_user_id()
)
);
}
return $args;
}
add_filter( 'get_terms_defaults','exclude_not_allowed_terms', 20, 2 );