The highest amount of local free energy are going to be in the transition states, due to the presence of partially formed bonds. The partially formed bonds do not contribute to the stability of the molecule, it is actually very high energy for the molecule to pass through this unfavorable state. In an intermediate then, there are formed bonds that will contribute to stability, and thus a lower local free energy. Dependent on the reaction (endothermic or exothermic), the intermediate will have higher or lower energy than its respective reactants or products, thus it is only locally that we find this stability.
below is a link to a nice picture of the reaction coordinate diagram describing what we see: https://www.cazypedia.org/index.php/Rea ... termediate