For some weird reason (I think it’s just me and lag but I don’t know since it’s never happened to me before in lag), the auto-scheduler somehow managed to schedule flights over other flights that were already happening or were going to happen. It even managed to schedule flights at a certain hour which already passed by. So it would end up looking as if two simultaneous flights were going to happen at the same time at the same gate. Nevertheless, once I found the problem I turned auto-schedule off.
Here is a picture of what it looks like on the flight planner:
I also created an in-game bug report, issue ACEO-23914