Limit and Offset breaks query with multiple non-join FROM statements

$query = $query->select('sf_guard_permission.id,
cms_section_translation.slug||\' \'||SUBSTRING("name", POSITION(\'@\' in "name") + 1) as name,
sf_guard_permission.description,
sf_guard_permission.created_at, sf_guard_permission.updated_at');
$query = $query->from('sfGuardPermission sf_guard_permission');
$query = $query->addfrom('CmsSection cms_section');
$query = $query->innerJoin('cms_section.WithCmsSectionTranslation cms_section_translation');
$query = $query->where('cast(SUBSTRING("name", 1, POSITION(\'@\' in "name") - 1) as integer) = cms_section.id');
$query = limit(20);
$query = offset(1);

Generated:

SELECT s.id AS s_id, s.description AS sdescription, s.created_at AS screated_at, s.updated_at AS supdated_at, c2.slug||' '||SUBSTR("name", POSITION('@' in "name") + 1) AS c2_0 FROM sf_guard_permission s, cms_section c INNER JOIN cms_section_translation c2 ON c.id = c2.sec_id WHERE s.id IN (SELECT doctrine_subquery_alias.id FROM (SELECT DISTINCT s2.id, c3.deleted_at FROM sf_guard_permission s2 cms_section c3 INNER JOIN cms_section_translation c4 ON c3.id = c4.sec_id WHERE cast(SUBSTR("name", 1, POSITION('@' in "name") - 1) as integer) = c3.id ORDER BY c3.deleted_at DESC LIMIT 20) AS doctrine_subquery_alias) AND (cast(SUBSTR("name", 1, POSITION('@' in "name") - 1) as integer) = c.id) ORDER BY c.deleted_at DESC

Notice:
SELECT DISTINCT s2.id, c3.deleted_at FROM sf_guard_permission s2 comma that is missing cms_section c3