Data Flow - Merge vs Merge as New

Our company has recently upgraded to Power BI pro and we are starting to experiment with Dataflows however, we are getting a strange error when trying to merge two entities. 

We have to entities that are part of the same database that we are pulling using SQL. Each of the tables we are pulling have the same field (known as EmployeeID). When we merge these tables as a new entity, we are able to publish and refresh the dataflow with no problems. However, when we try to merge the tables into one of the existing entities, we can publish but the refresh cancels itself after a few seconds. 

We have been unable to successfully refresh a dataflow that has two entities merged that were not merged as new. Below is a screen shot of the error received when trying to refresh. It appears that one entity refreshes and the other cancels itself.

Has anyone experienced this and/or found a solution? Thanks!