We notice that after deleting VMs or Files the free space on Nutanix cluster doesn’t  increase instantly and may only reflect after a few hours. 

This behavior of free space being slowly presented back to the cluster is expected behavior for Nutanix.

The reason for this is because of the service responsible for cleaning up space, Curator. Curator takes time to perform scans on the cluster and spreads the storage across the disks and carefully removes the correct files (egroups) while maintaining redundancy for any data you want to keep.

It takes a few curator scans before all expected free space is available again. Each curator scan is scheduled to be performed once per hour. To remove more data, it will take longer time for curator to clean up data relative to the existing workload of the cluster.

In case after 24 hours, the space is not reclaimed and does not appear as free space, contact Nutanix Support for assistance with diagnosing the cluster health.

Portal document explaining the same information  in a bit more detail is as follows:

https://portal.nutanix.com/kb/000002924