Models of actual causality leverage domain knowledge to generate convincing diagnoses of events that caused an outcome. It is promising to apply these models to diagnose and repair run-time property violations in cyber-physical systems (CPS) with learning-enabled components (LEC). However, given the high diversity and complexity of LECs, it is challenging to encode domain knowledge (e.g., the CPS dynamics) in a scalable actual causality model that could generate useful repair suggestions. In this paper, we focus causal diagnosis on the input/output behaviors of LECs. Specifically, we aim to identify which subset of I/O behaviors of the LEC is an actual cause for a property violation. An important by-product is a counterfactual version of the LEC that repairs the run-time property by fixing the identified problematic behaviors. Based on this insights, we design a two-step diagnostic pipeline: (1) construct and Halpern-Pearl causality model that reflects the dependency of property outcome on the component's I/O behaviors, and (2) perform a search for an actual cause and corresponding repair on the model. We prove that our pipeline has the following guarantee: if an actual cause is found, the system is guaranteed to be repaired; otherwise, we have high probabilistic confidence that the LEC under analysis did not cause the property violation. We demonstrate that our approach successfully repairs learned controllers on a standard OpenAI Gym benchmark.