With the rise in aviation demand and the emergence of Urban Air Mobility, developing a safe aviation system in urban areas is becoming increasingly important. This study addresses the challenge of detecting anomalous flight trajectories, which can be influenced by environmental factors. We propose a novel Long Short-Term Memory-Auto Encoder (LSTM-AE) model that processes both environmental and trajectory data but only reconstructs trajectory data in its output. This approach was validated by assessing the average reconstruction error for specific trajectories. Additionally, the model's ability to identify anomalies was confirmed by evaluating the Area under the ROC curve (AUC) for typical anomalous trajectories, such as go-around maneuvers. Our findings indicate that the proposed LSTM-AE model effectively learns trajectory patterns in relation to environmental variables and shows enhanced anomaly detection capabilities compared to traditional AE and LSTM-AE models. These results contribute to the development of advanced models that incorporate a wider range of environmental factors, enhancing safety in urban air travel.