Potential energy versus reaction coordinate (graph of Gibbs free energy)
There is a long explanation for that, however in short they are not the same thing. Free energy relates to thermodynamic systems with many particles and is governed by Boltzmann's distribution, a sum of all possible energy configurations, where F is the free energy of the system.

$Z = e^{- \frac{F}{kT}} = \sum_i e^{- \frac{E_i}{kT}}$

Potential energy is non-statistical and well-defined for one particle. Thermodynamic free energy (one type being Gibbs) is a subset of the total potential energy. Even though they may seem similar, they should not be confused and should not be interchanged.