The attempt to download the contents of a running virtual machine via the vSphere UI Data Browser results in a partial download only.
VCF 9.x
Downloading the files of a running virtual machine is not possible.
Additionally, downloading the virtual machine contents in this way is not a recommended/supported approach - it is a web browser limitation as to whether or not the download will be successful.
Stop the virtual machine that is running.
Once the virtual machine is stopped, either -
(1) right click the virtual machine in the vSphere UI > Template > Export OVF Template
or
(2) use WinSCP (or similar) to connect to the host, navigate to the relevant directory and download the files that way