The failure modes of molecular junctions have been only sporadically investigated, but they are important to understand so they can be prevented and molecular junctions can be optimized. Although it is commonly accepted that the performance and electrical characteristics of molecular tunneling junctions depend strongly on the supramolecular structure of the molecules inside the junctions, how sensitive molecular junctions are to small supramolecular changes and the factors that cause disorder are poorly understood for most types of molecular junctions. This paper shows that the performance of a large-area molecular diode depends on the choice of the anchoring group and solvent used for the formation of the self-assembled monolayer (SAM) in which both affect the surface coverage and the occurrence of disordered SAM domains. As a result, the rectification ratio was reduced by more than a factor of 10 across a series of molecular diodes, containing a diphenylacetylene backbone and a ferrocenyl terminus. The diodes failed because of leakage currents flowing across defective parts in the SAM lowering the rectification ratios, while the yield in working junctions or the electronic structure of the SAMs was remarkably insensitive to defects inside the SAMs. Thus, a judicious choice of anchoring group and solvent used in the SAM formation process can result in a 10-fold improvement in the performance of molecular diodes.