You noticed that employees are being replicated from CRM to C4C through the Business Partner Web Service (BusinessPartnerReplicationIn).
Employees need to be created via the employee replication service and not via the business partner replication service.
SAP Hybris Cloud for Customer Integration with SAP CRM
Business Partners with employee role are not filtered in CRM.
You must use the BAdI implementation CRMPCD_BUPA_MAP in order to avoid employees be replicated via business partner service.
See SAP Note 1964282.
KBA , LOD-CRM-INT-CRM , Integration of C4C with CRM , Problem