VMware released the ESXi 6.0 patch for CBT issue discovered few days ago that makes VMs incremental backups to be inconsistent.
The problem is related to the CBT API QueryDiskChangedAreas() call that sometimes returns incorrect changed blocks. Check out this post for the problem description.
The patch can be deployed through VMware vSphere Update Manager or downloading the .zip file from the VMware download page installing the VIB by using the esxcli software vib command.
Additional info about the patch can be found in the KB 2137545.