The weather phenomenon is predominant when it comes to drone warfare with characteristics like slow speed and weak SNR on track. Thus, the radars can confuse bird activity or weather phenomenon with low rcs and slow moving drones and vice versa.
Then you can tally the weather data with track data to validate whether it is indeed a valid target or not. e.g you would check the presence of clouds and wind direction and wind speed to tally with the movement, speed and height of track.
However, for fighters and large body aircrafts, you usually get solid tracks - again characterized by high speed, high SNR and distict flight profile and flight path.
Now add to it the facts that they were particularly firing S400s in a certain zone and this was a repeat episode and not just one odd incident.
So i believe, they were trying to do something deliberately and terminating own missiles mid flight (amritsar ones) which totally defies reasoning. lol