Use subqueries for each of GROUP_CONCATs:
SELECT i.id, i.title, i.items_title, f.filters_title FROM
( SELECT
projects.id,
projects.title,
GROUP_CONCAT(project_items.title) AS items_title
FROM projects
LEFT JOIN project_items ON project_items.projects_id=projects.id
group by projects.id,
projects.title) as i
INNER JOIN
( SELECT
projects.id,
projects.title,
GROUP_CONCAT(filters.title) AS filters_title
FROM projects
LEFT JOIN project_filters ON projects.id=project_filters.projects_id
LEFT JOIN filters ON filters.id=project_filters.filters_id
group by projects.id,
projects.title) as f
ON i.id = f.id
WHERE i.id="1"