When nanoparticle self-assembly takes place in an anisotropic liquid crystal environment, fascinating new effects can arise. The presence of elastic anisotropy and topological defects can direct spatial organization. An important goal in nanoscience is to direct the assembly of nanoparticles over large length scales to produce macroscopic composite materials; however, limitations on spatial ordering exist due to the inherent disorder of fluid-based methods. In this paper we demonstrate the formation of quantum dot clusters and spherical capsules suspended within spherical liquid crystal droplets as a method to position nanoparticle clusters at defined locations. Our experiments demonstrate that particle sorting at the isotropic-nematic phase front can dominate over topological defect-based assembly. Notably, we find that assembly at the nematic phase front can force nanoparticle clustering at energetically unfavorable locations in the droplets to form stable hollow capsules and fractal clusters at the droplet centers.