Modern mobile devices consists various sensors such as accelerometers and gyroscopes that can be used to aid and complement Global Navigation Satellite System position and velocity updates. Especially these sensors are now capable of providing good navigation solutions for pedestrians with competitive battery power consumption when compared to radio navigation systems. In order to achieve this energy efficiency, the navigation solutions could primarily be based on onboard inertial sensors alone, and additional aiding systems such as GNSS or indoor map used only when requested, such as to initialize the starting position. One of the most critical problems in such mobile device navigation solutions is the inability to accurately estimate the misalignment between the pedestrian walking direction and the mobile device orientation, eventually causing the navigation algorithm to output wrong location solution. In this paper we propose methods to detect such situations and means to reduce the errors due to the misalignment estimation error.