We consider a supervised learning setup in which the goal is to predicts an outcome from a sample of irregularly sampled time series using Neural Controlled Differential Equations (Kidger, Morrill, et al. 2020). In our framework, the time series is a discretization of an unobserved continuous path, and the outcome depends on this path through a controlled differential equation with unknown vector field. Learning with discrete data thus induces a discretization bias, which we precisely quantify. Using theoretical results on the continuity of the flow of controlled differential equations, we show that the approximation bias is directly related to the approximation error of a Lipschitz function defining the generative model by a shallow neural network. By combining these result with recent work linking the Lipschitz constant of neural networks to their generalization capacities, we upper bound the generalization gap between the expected loss attained by the empirical risk minimizer and the expected loss of the true predictor.