The Polyhedral Skeletal Electron Pair Theory (PSEP) which correlates the structural arrangement of clusters to their electron count does much for rationalizing the structures of a wide range of organometallic clusters. However, these rules based on the isolobal analogy principle apply less successfully to complicated compounds containing a heteronuclear core. Different tri- and tetranuclear organometallic compounds serve to illustrate some of the limitations of the PSEP theory to account for skeletal isomerism, isomer interconversion or unexpected geometries. Molecular orbital calculations are used to help and sometimes to circumvent some of these limitations.