The partially filled skutterudite structure is a candidate thermoelectric material with the capacity for phonon scattering by the decoupled rattling of filling ions. In this transmission electron microscopy investigation of a 1.6%Ce, 1.6%Ni, 4.9%Ge, 22.8%Co, and 69.1%Sb alloy, the structure is confirmed to be of a partially-filled skutterudite, but with a number of defects. Isolated dislocation dipoles, arrays of dislocation dipoles, and a subgrain boundary are observed and characterized. An atomic structure of a dislocation dipole is also proposed, and the effect of such dislocations on thermoelectric properties is discussed.