This is going to be related to Samba, vhd support, smb3, vss. 2012 R2 can do block level backups and sparse files. I'm not sure if even the latest Samba iterations allow the necessary functions, but it doesn't surprise me at all that this wouldn't work.
That's the vein I would research. Can't say I've worked through the problem though. One decent
technet thread.
Another thread here with the same problem. I think this will come in a later version of Samba to be honest and probably wouldn't fight super hard.