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One of the main challenges when working with time series captured online using sensors is the appearance of noise or null values, generally caused by sensor failures or temporary disconnections. These errors compromise data reliability and can lead to incorrect decisions. Particularly in the treatment of diabetes mellitus, where medical decisions depend on continuous glucose monitoring (CGM) systems provided by modern sensors, the presence of corrupted data can pose a significant risk to patient health. This work presents an approach that encompasses online detection and imputation of anomalous data using physiological inputs (insulin and carbohydrate intake), which enables decision-making in automatic glucose monitoring systems or for glucose control purposes. Four deep neural network architectures are proposed: CNN-LSTM, GRU, 1D-CNN, and Transformer-LSTM, under a controlled fault injection protocol and compared with the ARIMA model and the Temporal Convolutional Network (TCN). The obtained performance is compared using regression (MAE, RMSE, MARD) and classification (accuracy, precision, recall, F1-score, AUC) metrics. Results show that the CNN-LSTM network is the most effective for fault detection, achieving an F1-score of 0.876 and an accuracy of 0.979. Regarding data imputation, the 1D-CNN network obtained the best performance, with an MAE of 2.96 mg/dL and an RMSE of 3.75 mg/dL. Then, validation on the OhioT1DM dataset, containing real CGM data with natural sensor disconnections, showed that the CNN–LSTM model accurately detected anomalies and reliably imputed missing glucose segments under real-world conditions. Full article