Are you using the Online QEF program or the built in W2/1099 Reporter inside your program?
If you are using the QEF see this FAQ. It's a couple years old so I don't know if they fixed it yet. Let me know if it still prints one 1096 per person.
https://ttlc.intuit.com/questions/2620410-quick-employer-forms-printing-1096-for-each-1099-misc
