Copter flying to not set point

I fly on Orange Cube with Hex Core. My ground station is on UgCS and I upload missions from json format. I faced strange situation. My copter after uploading mission and turning on Auto mode starts to fly to point other than setted waypoints. It points to some point nearby. Never setted before. It shows when it should do takeoff action while in flight. Has some one encountered this error or know any reason why it happens?

Post more details and a .bin file

This are two logs from two flights were it occured and image describing the situation.
While drone was in the middle air, it was stopped at the point 1. Then we uploaded new trajectory. His first point was takoff to desired height. Usually it was flying to the first waypoint marked as 2. The UAV instead of flying to point 2 started to fly to point 3, which is not on the planned trajectory. Does anybody has this problem before? I also uploaded trajectory uploaded from flight controller by Mission Planner. The thing that conserns me is occurance of NaN values. Thanks in advance for help.

Does my information clarified the problem?