Sometimes, backup at a hypervisor level is not possible because of virtualization product limitations.
VMware vSphere does not support snapshots of fault tolerant virtual machines, independent disks, and Raw Device Mapping (RDM) disks in physical compatibility mode.
Microsoft Hyper-V does not provide control over pass-through disks to a host system. As a result, the Microsoft Software Shadow Copy provider cannot provide Agent for Hyper-V with snapshots of pass-through disks.