When merging 2 records together that also share a household, the household record is the source record and the target record. Based on the merged configuration, both records in the household should be the source records.
We're currently evaluating this issue for a fix in a future patch or service pack.
Steps to Duplicate
Go to Constituents > Add an Individual
Enter the first and last name (For example, Wife Source) and click Save
Select the Relationships tab > Add Individual
In the Related Individual field, click the binoculars and click Add
Enter the first and last name (For example, Husband Source) and click Save
Select a value for the relationship types
Mark "this is the spouse relationship for RECORD NAME" and "These Individuals are members of the same household" checkboxes
Repeat the same steps as above to create the target records. (For example- Wife Target and Husband Target)