생성된 쿼리에 "order by"에 "documents.list_order" 때문에 문제가 생깁니다.
"comment.list_order"가 맞는데...
xml 파일에는 "comment.list_order"로 입력 돼있습니다.
소스상에서 "documents"로 바꾸는것 같네요.

modules/document/queries/getDocumentListWithinComment.xml
 <query id="getDocumentListWithinComment" action="select">
    <tables>
        <table name="documents" alias="documents" />
        <table name="comments" alias="comments"/>
    </tables>
    <columns>
        <column name="documents.document_srl" />
        <column name="comments.list_order" />
    </columns>
    <conditions>
        <condition operation="in" column="documents.module_srl" var="module_srl" filter="number" />
        <condition operation="equal" column="documents.category_srl" var="category_srl" pipe="and" />
        <condition operation="equal" column="documents.document_srl" default="comments.document_srl" notnull="notnull" pipe="and" />
        <condition operation="equal" column="documents.member_srl" var="member_srl" filter="number" pipe="and" />
        <group pipe="and">
            <condition operation="more" column="documents.list_order" var="division" pipe="and" />
            <condition operation="below" column="documents.list_order" var="last_division" pipe="and" />
        </group>
        <condition operation="like" column="comments.content" var="s_comment" notnull="notnull" pipe="and" />
    </conditions>
    <navigation>
        <index var="sort_index" default="comments.list_order" order="asc" />
        <list_count var="list_count" default="20" />
        <page_count var="page_count" default="10" />
        <page var="page" default="1" />
    </navigation>
    <groups>
        <group column="documents.document_srl" />
        <group column="comments.list_order" />
    </groups>
</query>


modules/document/document.model.php
             // document.getDocumentList 쿼리 실행
            // 만약 query_id가 getDocumentListWithinComment 또는 getDocumentListWithinTag일 경우 group by 절 사용 때문에 쿼리를 한번더 수행
            if(in_array($query_id, array('document.getDocumentListWithinComment', 'document.getDocumentListWithinTag'))) {
                $group_args = clone($args);
                $group_args->sort_index = 'documents.'.$args->sort_index;
                $output = executeQueryArray($query_id, $group_args);
                if(!$output->toBool()||!count($output->data)) return $output;

                foreach($output->data as $key => $val) {
                    if($val->document_srl) $target_srls[] = $val->document_srl;
                }

                $target_args->document_srls = implode(',',$target_srls);
                $target_args->list_order = $args->sort_index;
                $target_args->order = $args->order_type;
                $target_args->list_count = $args->list_count;
                $target_args->page = 1;
                $output = executeQueryArray('document.getDocuments', $target_args);
            } else {
                $output = executeQueryArray($query_id, $args);
            }

생성된 쿼리
 SELECT FIRST 20 SKIP 0
    "documents"."document_srl",
    "comments"."list_order"
FROM
    "xe_documents" as "documents",
    "xe_comments" as "comments"
Where
    ("documents"."module_srl" in (58) and
    "documents"."document_srl" = "comments"."document_srl" and
    "comments"."content" like '%댓글%') and
    ("documents"."list_order" >= -102)
GROUP BY
    "documents"."document_srl",
    "comments"."list_order"
ORDER BY
    "documents"."list_order" asc