Jesus is describing the dispersal of the remaining three tribes, because the dispersal of the Northern House of Israel (10 tribes) had happened in 722 B.C. All of the 12 Tribes were known to be dispersed, however, even before the destruction of the 2nd Temple in 70 AD, as James states in the first verse of his epistle "to the 12 tribes scattered abroad."  It is not likely that James wrote this after 70 AD, though it is possible according to some scholars. Regardless, the 3 tribes you refer to  (Benjamin, Judah, and Levi, or 'the house of Judah') were scattered to Babylon in the 6th C. B.C. and never fully returned, always leaving a remnant of them scattered.  

This passage is clearly referring to the house of Judah (Benjamin, Judah, and Levi) exiled in 70 AD.