We also have a similar issue.
Dataset P_Invoice
Dataset P_SalesOrder
We joined these in a DirectQuery for Report1.
***Months later we added measure 'Count of Customers' to P_Invoice and P_SalesOrder.
Then we go back to do some basic maintenance on Report1. We hit Refresh on the desktop file and we get the dreaded message...
DirectQuery to AS - P_Invoice
'The name 'Count of Customers' is already in use for a measure on the table 'Invoice'. Choose a different name.
DirectQuery to AS - P_SalesOrder
'The name 'Count of Customers' is already in use for a measure on the table 'Invoice'. Choose a different name.
For clarity sake, table 'Invoice' only exists in P_Invoice. However, both datasets had measure 'Count of Customers' added to them after we initially made Report1.
I think Power BI has no problem with the same measure name across datasets in a DirectQuery as long as they exist when the DirectQuery is created. But when measures with the same name are added later it doesn't know how to handle it.
We've been dealing with this by simply deleting the datasets used in the DirectQuery and reconnecting to them. No problems except it's a pain rebuilding the report and whatever may have broken.