They might be the legitimate person but believe me any person would get scared after seeing 3 policemen poking into his car and searching for something, given the law in situation in our country, the behaviour of police and the situation of low order courts.
BTW they might have been some thieves because they only wanted to check the owner of the car and also its ownership status. Who knows they might have said to you that look there is a problem in our network and we have to go to the nearby police station to verify, for that you have to follow us in our car. They than lead you to a deserted place and than get out of their car and on gun point snatch your car and run away. What can one do write down the registration number of that private car but you know it hardly takes 5 minutes to replace both number plates.
The best one can do is that let them check your car and always carry photocopy of documents in your car. Also keep noting their actions if they just check the number and insert it in laptop on mtmis website it would show the records as per the website records. And those records are mostly not upto date so its better to keep copies of taxation documents with you.
I was once stopped by 4 man travelling in a chitti cow with a blue siren on its roof. They were in civilian dress. At that time I was leaving lahore with my family the time was 7am. They signalled me to stop and asked me for ID. I at once presented them my NIC, and they were satisfied. Actually they were looking for a honda city being stolen from airport area with the same color as my car. They also asked have I come from the airport as I had lugguage but I said no I am going to sahiwal that is why I have lugguage. So they left me.