Mean field games (MFGs) describe the collective behavior of large populations of interacting agents. In this work, we tackle ill-posed inverse problems in potential MFGs, aiming to recover the agents' population, momentum, and environmental setup from limited, noisy measurements and partial observations. These problems are ill-posed because multiple MFG configurations can explain the same data, or different parameters can yield nearly identical observations. Nonetheless, they remain crucial in practice for real-world scenarios where data are inherently sparse or noisy, or where the MFG structure is not fully determined. Our focus is on finding surrogate MFGs that accurately reproduce the observed data despite these challenges. We propose two Gaussian process (GP)-based frameworks: an inf-sup formulation and a bilevel approach. The choice between them depends on whether the unknown parameters introduce concavity in the objective. In the inf-sup framework, we use the linearity of GPs and their parameterization structure to maintain convex-concave properties, allowing us to apply standard convex optimization algorithms. In the bilevel framework, we employ a gradient-descent-based algorithm and introduce two methods for computing the outer gradient. The first method leverages an existing solver for the inner potential MFG and applies automatic differentiation, while the second adopts an adjoint-based strategy that computes the outer gradient independently of the inner solver. Our numerical experiments show that when sufficient prior information is available, the unknown parameters can be accurately recovered. Otherwise, if prior information is limited, the inverse problem is ill-posed, but our frameworks can still produce surrogate MFG models that closely match observed data.