The quantum states in metal clusters are bunched into electronic shells as in atoms. Ligands including halogens or thiols modify the electronic structure through bonding, resulting in stable clusters with filled electronic shells that are resistant to oxygen etching. We demonstrate that the stabilization afforded by ligands is partially confounded because the ligands perturb the charge density of the metallic core, inducing Lewis acid-base sites that make the cluster reactive in a protic environment. We demonstrate the importance of induced active sites by studying the reactivity of methanol with two classes of iodine-passivated aluminum cluster anions: Al13Ix-, which has a closed geometric shell, and which has an adatom-decorated core. Two adjacent ligands on the closed geometric shell of Al-13(-) activate the cluster, while in Al14I3- the I induces an active site on the adatom, making the cluster reactive, explaining ligand-protected clusters' preference for closed geometric shells.