Hello Jojje,
This should not happen in datasources, which were created with OPM SS5R or later, because there is an Unique tag added on the GUID field in DB, and DB Engine will not allow duplicate entries in there.
If I remember, on your site we did the cleaning, but did not implement the scripts which should create unique index for GUID field, because you needed some help from DBA on that. Could it be the case that you have never added those indexes to your DB in the end?
Let me know if you'd need more help with that.
Regards,
Justinas