VMware acknowledged a known issue within ESXi 6.0 and 6.0 U1. Changed Block Tracking (CBT) looses the information of I/Os during snapshot consolidation. The main backup isn’t affected but all data written during the consolidation task are missed.
ALL CBT incremental backups are potentially affected.
This issue is resolved in VMware ESXi 6.0 patch ESXi600-201511001. For more information, see VMware ESXi 6.0, Patch Release ESXi600-201511001 (2137545).