|14You shall provide the three cities in trans Jordan and the three cities in the land of Canaan; they shall be cities of refuge.||ידאֵת | שְׁלשׁ הֶעָרִים תִּתְּנוּ מֵעֵבֶר לַיַּרְדֵּן וְאֵת שְׁלשׁ הֶעָרִים תִּתְּנוּ בְּאֶרֶץ כְּנָעַן עָרֵי מִקְלָט תִּהְיֶינָה:|
|the three cities: Although there were nine tribes in the land of Canaan, and here [across the Jordan] there were only two-and-a-half, He equalized the number of their refuge cities, because Gilead had many murderers, as it says,“Gilead, a city of workers of violence, who lurk to shed blood” (Hos. 6: 8). - [Mak. 10a, Sifrei Massei 6]||את שלש הערים וגו': אף על פי שבארץ כנען תשעה שבטים וכאן אינן אלא שנים וחצי, השוה מנין ערי מקלט שלהם משום דבגלעד נפישי רוצחים, דכתיב (הושע ו, ח) גלעד קרית פועלי און עקובה מדם:|
My grandfather quotes the above and the Ramban who starts his explanation by citing Rashi as well and then saying that even though the cities were meant for those who were only guilty of manslaughter and not of murder, intentional murderers would act with cunning to present themselves as guilty of the lesser crime and go to the cities of refuge. The Ramban says that he is astounded at the stated problem of the equation for the number of cities, though. There were an additional 42 cities of refuge due to the Levi cities serving as such: 36 in Israel proper and another 6 to the east.
My grandfather points out that there is some different between the Levi cities and the designated cities of refuge, for the halacha is like R' Yehudahs that in the 42 cities the Leviim received rent, though not in the 6. Consequently, the split still shows a disproportionate number of designated cities of refugees per capita for the east, which is explained by the greater incidents of bloodshed there.
He suggests an answer that he later found in the Divrei David. The need for more cities of refuge in a place where there is a higher homicide rate is due to the fact that anyone who killed someone -- whether intentionally or unintentionally -- would run to a city of refuge. [Later it would have to come to light if the killer had witnesses who can attest to the status of murder or manslaughter.]
Related post: http://kallahmagazine.blogspot.com/2015/10/dvar-yehudah-parsha-points-from-my.html