When using the Segmentation feature, Constituents that appear in multiple input queries within the segmentation, will only appear within the top output query for the segmentation.

For Example:
Input Query 1 includes these records:
John Jones
Sabrina Smith
Rachael Turner
Sean Jackson

Input Query 2 includes these records:
John Jones
Sabrina Smith
Rachael Turner
Sean Jackson
Robert Johnson

Output Query 1 will include
John Jones
Sabrina Smith
Rachael Turner
Sean Jackson

Output Query 2 will ONLY include
Robert Johnson

This is working as designed.  
The segmentation feature will not produce duplicates within the Output queries.  If a record exists in an Input query that is higher in the segmentation, they will only be in that Output query.  They will not appear in the subsequent Output queries.