we had case 02308849 for this. response below:
"Veeam agent is entirely cluster unaware- https://www.veeam.com/kb2304
Presenting the drives as internal disks lets us leverage VSS against them, but underneath in the real world they're still cluster shared volumes. Veeam has no idea that any other nodes exist, but the data's constantly being accessed and replicated and manipulated between the nodes. This is expected behaviour for this set up. The blocks are changing as far as veeam can tell from looking at the windows master file table, because as far as windows is concerned, things are moving around and being changed."
long story short, this is actually a VM running Hyper-v 2012 R2 cluster (so on clustered volumes) and the VM itself is part of a DAG. We were forced to use the agent as currently we cannot snap the VM with the Veeam console (fails to take a snap of the VM at hypervisor level). But that it's a diff story.