An important step in Monte Carlo treatment planning (MCTP), which is commonly performed uncritically, is segmentation of the patient CT data into a voxel phantom for dose calculation. In addition to assigning mass densities to voxels, as is done in conventional TP, this entails assigning media. Mis-assignment of media can potentially lead to significant dose errors in MCTP. In this work, a test phantom with exact-known composition was used to study CT segmentation errors and to quantify subsequent MCTP inaccuracies. For our test cases, we observed dose errors in some regions of up to 10% for 6 and 15 MV photons, more than 30% for an 18 MeV electron beam and more than 40% for 250 kVp photons. It is concluded that a careful CT calibration with a suitable phantom is essential. Generic calibrations and the use of commercial CT phantoms have to be critically assessed.