They may have sent her through secondary with you for your convenience since you were traveling together and some couples may have a meltdown if they are separated for more than five minutes.

Also, if the inspection gave them cause to believe you would be smuggling something, then they might want to search her bags too, since you presumably could have stashed something in her bags.

You say you still don't understand what they were doing with your passport. They were looking up information about you, as I said in my prior post. That information must have been boring, as it gave them no cause to search your bags, other than the x-ray.