Issue is that the schedule changes are progressively done over course of day. At one moment one of your flights may have no longer shown as available or connection drops below MCT, etc. Rebooking can only go by what is currently showing in system as available. Thus for example when 1st of 2 connecting flights time changes so dont meet MCT, system reboots you. However then your 2and connection changes enough you would meet MCT. However for a period of minutes/ hours it looked like you didn't so were rebooked. Also flight number changes essentially are viewed as flight cancellations. System looks to rebook you, and it can happens before new flight is loaded.