If you download the drilldown of the Virtual Machine cost in Cost History, you will note that this cost consists of several services (Bandwidth, Virtual Machines, Virtual Machines Licenses, and Virtual Network):
The VM Cost report on the other hand only includes the Virtual Machines costs, and excludes Bandwidth, Virtual Machines Licenses, and Virtual Network. Therefore, if you remove these services from the drilldown csv from Cost History the sum should match the VM Cost report.