I experimenced same behavior on ispconfig Version: 2.2.40
I must go directly to database, exacltly to `isp_isp_domain` and delete this bad asociated co-domain, was asociated to another website, and using GUI i dont have privileges to modify...wtf...so i delete them in databse and using GUI create to correct websites. Workaround, but worked.
But i realy cannot simulate that again. That must be error in time of save.