If you have 1 employee and that employee is "in" more than 1 department. As long as you include Employee and Department tables in your query, and ask for employee and department you will see that employee in each department he/she is "in".
Suppose you had a query that asked which employee is the "Emergency Responder" for each department (and John Doe is your Employee who is in more than 1 department)
Dept 1 --John Doe
Dept 2 --Sue Schmidt
Dept 3 --Joe Blow
Dept 4 --John Doe
Dept 5 --Patty Kake
It isn't that John Doe is duplicated, the reality is he is the employee that has been designated as Emergency Responder for Dept 1 and also for Dept 4. And the query asks for Dept and Employee.
Now if you asked, What are the Distinct Names of Emergency Responders (no department reference) you would only see John Doe once.
Note also, a duplicate in a query response, requires that there all fields in the response have the same value. Said differently, if you have a duplicate, you would have 2 rows returned and corresponding fields in each row would have the same value.
In your case
Dept 1 John Doe is NOT a duplicate of
Dept 4 John Doe.
Duplicate would be
Dept 1 John Doe
Dept 1 John Doe
or
Dept 4 John Doe
Dept 4 John Doe