1) Mount DB2 database using RDMs or NFS and backup VM and DB2 database separate (this is the recommendation as it is more granular backup / restore for both and simplest to setup)
2) Backup DB2 database and VM together. For this the DB2 database must be installed in the VM partition itself. So if the VM has a C: drive you would install DB2 DB directly there.
What we dont support and what we know has issues is using virtual disks which is my guess to above problem. We also dont support backing up app + vm together when app is installed on separate disks RDMs, NFS, or virtual disks.