@jkeckard007
I think you'll need @Pstork1 to provide some more guidance here... but I think you'll need to do the following:
1. Delete the 'Apply to each 2' and 'Apply to each 3' (and contained actions)
2. Re-add a 'Condition' action directly underneath the second 'Get Items' action
3. Select the 'Employee ID' value from the 'Get Items 1 and compare to the the 'Employee ID' value from the 'Get Items' 2... that should set the loop up correctly.
This will find duplicates but its a pretty expensive query, and it won't work for large lists (above 5000) even after enabling pagination... Working with @Pstork1 excellent suggestion I updated to the following but it still suffers the same limitation with the original query... the second query is slightly quicker as it will return a smaller result set and only do something if the array is greater than 1... i..e a duplicate exists.

This is still not really correct and needs more logic to be added a single duplicate would result in 2 separate emails (One for each duplicate item)... if your list contains less than 5000 items this may work, but I'd really suggest disabling duplicates on the list as per my original suggestion.
If you're list is above 5000 items I think will need a direct REST query using a CAML query to perform a GroupBy type query (I know distinct isn't support by ODATA)...
HTH
Jay