I have had the lids pop right when I am taking them out or when they are on the counter afterwards. I don't think they press down in the pot, that is, you should hear each one ping when they come out. Count as you take them out to hear all the pings. Sometimes you won't hear some of them but you will be able to tell if they sealed by lifting them by the lid on the next day. But if they all ping then you know they are fine. I count mine out loud as I hear them ping.
I don't think there is any harm in keeping the jars in a little longer. Maybe in doing pickled things they will be more cooked and soggy, otherwise I don't see a problem. I sometimes add a minute or two.
