Hi Carino,
I too use Lammps on Yosemite+MATLAB 2015a+Xcode and also have developed few mex based codes to post-process Lammps output with simulations.
I don’t think it is graphics issue but not sure.
Not aware of what exactly your matlab code tries to do but if it is happening
on the same Matlab on same system with same matlab file, sometimes a
“clear” command helps.
Still I don’t understand if you r getting segmentation fault for LAMMPS or for MATLAB!!