This article investigates the causes of occasional flight instability observed in Unmanned Aerial Vehicles (UAVs). The issue manifests as unexpected oscillations that can lead to emergency landings. The analysis focuses on delays in the Extended Kalman Filter (EKF) algorithm used to estimate the drone's attitude, position, and velocity. These delays disrupt the flight stabilization process. The research identifies two potential causes for the delays. First cause is magnetic field distrurbances created by UAV motors and external magnetic fields (e.g., power lines) that can interfere with magnetometer readings, leading to extended EKF calculations. Second cause is EKF fusion step implementation of the PX4-ECL library combining magnetometer data with other sensor measurements, which can become computionally expensive, especially when dealing with inconsistent magnetic field readings. This can significantly increase EKF processing time. The authors propose a solution of moving the magnetic field estimation calculations to a separate, lower-priority thread. This would prevent them from blocking the main EKF loop and causing delays. The implemented monitoring techniques allow for continuous observation of the real-time operating system's behavior. Since addressing the identified issues, no significant problems have been encountered during flights. However, ongoing monitoring is crucial due to the infrequent and unpredictable nature of the disturbances.