PDOException in EntityAPIController->query()

When editing a content type that has field collections with entities I seem to get the following error:

PDOException: SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '))' at line 2: SELECT revision.revision_id AS revision_id, base.item_id AS item_id, base.field_name AS field_name, base.archived AS archived, CASE WHEN base.revision_id = revision.revision_id THEN 1 ELSE 0 END AS default_revision FROM {field_collection_item} base INNER JOIN {field_collection_item_revision} revision ON revision.revision_id = base.revision_id WHERE (base.item_id IN ()) ; Array ( ) in EntityAPIController->query() (regel 187 van /Applications/AMPPS/www/work/drupal/d7/website/sites/all/modules/contrib/entity/includes/entity.controller.inc).

This seems to only happen when editing, not for newly created items.