There must be a duplicate record in the isp_dep database table. This table holds the relations between records.
1) Make a backup of the ispconfig database.
2) Login with phpmyadmin to the ispconfig db and search for the website that shows the wrong link in the isp_isp_web table, write down the doc_id and doctype_id of that record.
3) now search for the duplicate record. Replace 123 with the doc_id that you found in 2):
select * from isp_dep, isp_isp_domain WHERE isp_dep.child_doc_id = isp_isp_domain.doc_id AND isp_dep.child_doctype_id = 1015 AND isp_dep.parent_doc_id = 111
you will get several lines and one line for the wrong co-domain, note the dep_id of that wrong record and then delete the record with that id in the isp_dep table.