When checking the logs on my Enterprise Manager, the logs are filled with warnings such as: 

[WARN] [Smartstor/Superstor Spool] [Manager] Metric key id 0xb11111111 illegally used by two metrics: [SuperDomain/MyNameHere|Custom Metric Host (Virtual)|Custom Metric Process (Virtual)|Custom Metric Agent (Virtual)Calculator Output] and [SuperDomain/MyOtherNameHere|Custom Metric Host (Virtual)|Custom Metric Process (Virtual)|Custom Metric Agent (Virtual)Calculator Output]; ignoring second. 

  How can I stop these warnings from appearing in my EM logs?

Any version of APM 10.x

  This error is caused by multiple metrics trying to write to the same destination name.

  To fix this problem - look in your management modules for calculators that are creating metrics for the same destination name - then modify the destination name to be different for each calculator.

Once the destination metric name is unique, the warnings will stop.