I think that the unusual expression, "v'El Amo Tevi'enu" -- i.e., restore him to his people -- led to Chazal understanding this Derashah regarding Yehudah, since it implies that he was excommunicated and therefore needed restoration to his people. Since Moshe is praying long after Yehudah's death, the implication is that his death did not cancel the excommunication, and therefore Chazal say that his bones had not found rest.

However, the reason for the excommunication is unclear. Some authorities (see Rabeinu Bachye to Bereishis 45:24 and Devarim 33:7, and the Or ha'Chayim) see it as stemming from Yehudah's assertion that if he did not bring Binyamin he would be deemed "sinning to my father forever." In the end, Binyamin was restored to his father but the curse stayed on Yehudah and it is a form of excommunication.

It is also possible that Yehudah's excommunication stemmed from his being the leading protagonist in selling Yosef. In this case, Yehudah went against his personal attribute of taking responsibility (as he did for Tamar) and was therefore punished by being excommunicated. This is hinted at in the verse in, "And Yehudah descended from his brothers " (Bereishis 38:1) -- i.e., he was ostracized by them and left them. This is borne out by the Gemara (Makos 11b) which first suggests that Yehudah was punished for his statement regarding Binyamin, and then, in an alternative explanation, it mentions the concept of his bones not finding rest, seemingly for a different reason.

Yoel Domb