Rava says that Rabbis from Shevet Yissacher and Levi are better at Halachic issues. I was under the impression that the whole Shevet Yissacher disappeared hundreds of years before this. Were some of them still around or was this a tradition that Rava had?
I assume that you are referring to the fact that the "Aseres ha'Shevatim" -- "Ten Tribes" were sent into exile, and according to many sources in Chazal ended up across the River Sambatyon. Although this is true, there were some people who belonged to these Shevatim and avoided this exile, such as people from these Tribes who lived among Yehudah and Binyamin. [There are similar Gemaras in many places, such as the Gemara in Pesachim (4a) stating that someone was found to be from Shevet Zevulun].
All the best,