The Sanhedrin of Binyamin insisted that they would take care of the matter and would not allow the judges of the other tribes to "interfere". The other tribes insisted that because this was similar to what happened in S'dom, it had to be handled by the unified batei din of all the tribes (or a national Sanhedrin). Note that the incident itself was not the same as the incident of S'dom since only a few evil people acted in this way. The tribes were also punished for overreacting in this way by losing the first battles.
IIRC the actual problem was the disunity among the tribes and that "each man acted as seemed best in his eyes" (paraphrase). It was this disunity, which was like what led to the sale of Yosef, which led to the punishment.
As @AKayser points out, Binyomin had not been involved in the sale of Yosef, but we see that the same flaw that existed then existed now. Perhaps it is like Yosef bringing "dibasam ra" to his father.
We should also note, that the flaw may have been one that we do not fully notice and would not have been accounted a fault in Binyamin himself. From the way I read the story, it was the flaw in Bnei Yisrael that led to the end of the era of the Shoftim and the necessity for a melech. As a result, the particular case was the final straw in exhibiting that fault. Consider that right after getting the Torah, Bnei Yisrael were besieging Moshe with court cases. This tendency eventually led to the civil war.