Você precisa fornecer um alias à tabela de usuários na segunda vez que ingressar nela
por exemplo.
SELECT article . * , section.title, category.title, user.name, u2.name
FROM article
INNER JOIN section ON article.section_id = section.id
INNER JOIN category ON article.category_id = category.id
INNER JOIN user ON article.author_id = user.id
LEFT JOIN user u2 ON article.modified_by = u2.id
WHERE article.id = '1'
