We describe the characterization of structural defects that occur during molecular beam epitaxy of topological insulator thin films on commonly used substrates. Twinned domains are ubiquitous but can be reduced by growth on smooth InP (111)A substrates, depending on details of the oxide desorption. Even with a low density of twins, the lattice mismatch between (Bi,Sb)2Te3 and InP can cause tilts in the film with respect to the substrate. We also briefly discuss transport in simultaneously top and back electrically gated devices using SrTiO3 and the use of capping layers to protect topological insulator films from oxidation and exposure.