When viewing metrics from MQ Monitor, there is a difference between what you see under the real agent and under a virtual agent.
We can assume in this scenario that the virtual agent is only matching one MQ Monitor agent, the virtual agent is used to copy the metrics from SuperDomain to a custom domain for security purposes.
Metrics for Enqueue Count, Dequeue Count and Rate of Queuing all show double values in the virtual agent.
Other related metrics such as Enqueue Count Per Day show the same values in the real as the virtual agent.
In this situation, the agentclusters.xml had been copied to the collectors as well as the MOM. This was leading to these values being combined for certain metrics.
The solution was to make sure the agentclusters.xml is only configured on the MOM, which is the intended design of the file.