"when we shut down the two servers that are on the same subnet together the cluster shuts down and should remain online, as we have a witness files share.
when we turn off one of the servers that are on the same subnet, we wait and turn off the other and the third node that is on another subnet is able to keep the cluster online."
This sounds absolutely normal. Since Windows Server 2012, clusters have the ability to have a dynamic quorum. In other words, the number of nodes required for quorum changes as the number of nodes in the cluster changes. In your first situation you have a cluster with an odd number of nodes, so the witness does not contribute a vote to the quorum because you have a sufficient of nodes to maintain quorum (two) should a single node fail. But shutting down two nodes, you are leaving a cluster with a single node and a quorum count of one, so the cluster stops.
In your second situation, you shut down a single node and wait before shutting down the second node. What happens there is that when you shut down the single node, the witness now becomes a quorum member. Your quorum remains at two, but now the witness can provide a vote. When the second node is shut down, the witness keeps the quorum at two and the cluster continues.
The issue is shutting down the two nodes at the same time. That does not allow the dynamic quorum to adjust for the loss of a single node. In the second case where you wait between shutting down the nodes, the witness jumps in to provide the needed quorum vote. In your first situation you created a double failure by shutting down both nodes. In your second situation, by waiting between shutting down the two nodes, you allowed the dynamic quorum capability to keep the cluster running.
see https://video2.skills-academy.com/en-us/windows-server/failover-clustering/manage-cluster-quorum?source=docs for information on managing quorum within a cluster.
