We tested whether pilots would detect low-salient controllability problems more quickly during manual compared to automated flight. Using a moving-base simulator and a Piper Seneca aerodynamic model, airline pilots (n = 20) performed scenarios in which either a gradually ensuing single-engine failure or an icing accumulation occurred. Both scenarios were performed once during manual flight and once during automated flight, and were alternated with distraction scenarios. The icing accumulation was detected marginally significantly more quickly during manual flight, while there was no significant difference for the engine failure. Problems in manual flight were, as expected, most likely discovered from aircraft motions or control forces. Interestingly, there were several late detections during manual flight which appeared to be caused by subconscious manual corrections. In automated flight, the engine failure was discovered most often from the engine manifold pressure indication, while the icing accumulation was most often discovered from control column movement. The results therefore underline the importance of using back-driven controls, and further indicate that manual flight does not necessarily improve detection of problems that occur without display indications.