in 48:21 Yaakov tells Yosef, "ואני נתתי שכם אחד על אחיך" and Rashi explains that he actually gave to Yosef the city of Shchem which was above his regular portion which he was to receive.
Why Shchem? He could have given Yosef a different city as a gift. Why Shchem? Shchem, if it should have gone to anybody outside his inheritance, should maybe have gone to Shimon or Levi who destroyed it to save their sisters honor. Why would Yaakov give Shchem to Yosef?
Also, I looked at a map (not a great one) delineating the portions of the tribal divisions in Israel. Shchem is inside the portion of Menashe. So it was not really above and beyond the inheritance of Yosef. It was part of his portion anyways? Unless you say that the area of Shchem was not supposed to be part of Menashe (I guess it would have gone to Binyamin whose region borders Menashe's) but more land was included for contiguity between the rest of Menashe and Shchem...