The restaurant in the opening scene - supposedly set in Argentina - was actually in Malibu and Bruce Willis and his kids had been dining in there whilst filming was taking place. Jennifer Garner made a point of going in and saying hello.
When Marshall Flinkman is providing Sydney with background on the mysterious international terrorist Vadik, Marshall refers to two major crimes attributed to Vadik. The first is a major bombing in Pakistan; the second is the assassination of the Premier of "Kafiristan". Pakistan is, of course, a real country. "Kafiristan," however, is a fictitious place - but not one invented for Alias. It's an homage to both Rudyard Kipling and John Huston. "Kafiristan" was the fictional Himalayan country to which Kipling and Houston's heroes Peachy and Carney ventured off to become Kings of, in The Man Who Would Be King (1975).