Robots operating in real world settings must navigate and maintain safety while interacting with many heterogeneous agents and obstacles. Multi-Agent Control Barrier Functions (CBF) have emerged as a computationally efficient tool to guarantee safety in multi-agent environments, but they assume perfect knowledge of both the robot dynamics and other agents' dynamics. While knowledge of the robot's dynamics might be reasonably well known, the heterogeneity of agents in real-world environments means there will always be considerable uncertainty in our prediction of other agents' dynamics. This work aims to learn high-confidence bounds for these dynamic uncertainties using Matrix-Variate Gaussian Process models, and incorporates them into a robust multi-agent CBF framework. We transform the resulting min-max robust CBF into a quadratic program, which can be efficiently solved in real time. We verify via simulation results that the nominal multi-agent CBF is often violated during agent interactions, whereas our robust formulation maintains safety with a much higher probability and adapts to learned uncertaintie