I made the problem known on the official github but the person can't reproduce the problem, and told me to try one already built from libretro. In trying it out, i get the error relocation error: /opt/retropie/libretrocores/lr-snes9x/snes9x_libretro.so: symbol _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_replaceEjjPKcj, version GLIBCXX_3.4.21 not defined in file libstdc++.so.6 with link time reference
Might this be a reference to not having the latest gcc?