Error: Subquery returned more than 1 value. This is not permitted when the subquery follows =, !=, <, <=, >, >= or when the subquery is used as an expression. Due to having duplicate primary contacts for relationship with organization.

When adding a two different relationships to a organization record with the same constituent, then adding them both as a primary contact on the constituents record causes them to be both a primary record on the organization page. 
We are currently evaluating this issue for a fix in a future service pack.

Steps to Duplicate

1. Search for organization
2. Click relationships tab & click Subtab Relationships
3. Add individual, only adding the individual and the relationship
4. Now add the same individual again, only adding the individual and a different relationship
5. Go to the constituent's page you just added twice
6. Click relationships tab & click subtab relationships
7. Edit the organization relationship
8. Click the contact information tab
9. Add constituent as a contact and click checkbox for Primary contact
10. Repeat steps 7 - 9 for the same organization but different relationship
11. Note that on this tab you see only one Primary contact
12. Go back to the organization record
13. Click relationships tab & click subtab relationships
14. See that the constituent is listed as a Primary Contact twice
15. Click Analysis tab
16. Create constituent ad-hoc query
17. Include the Lookup ID to equal organization & Results fields to display 'Contact(Primary)\Constituent record
18. Click Preview results
19. Error occurs

Environment

 Blackbaud CRM
 4.0
 4.0.180.1600

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