VMware acknowledged a known issue (KB2136854) within ESXi 6.0 and 6.0 U1. 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.

VMware currently has no resolution.

Update 25.11.2015:

VMware released a patch for the CBT bug.

VMware ESXi 6.0, Patch ESXi600-201511401-BG: Updates esx-base (2137546)

Possible workarounds before intall the patch are:

VMware Resolution

If you are using Veeam for your backups, you can disable the CBT feature to remain consistent.

  • Edit Backup Job
  • Select Storage
  • Click on Advanced button
  • Go to vSphere tab and deselect Use changed block tracking data (recommended) and click on OK then Finish.