I see it sometimes arriving at foreign airports such as Paris. Transit passengers in some cases need visas and I presume the checks are to see if arriving transit passengers have the appropriate visas. In the US everyone needs to go through immigration so there is less reason for at the gate passport checks on arrival, but still given the possibility for error if they are looking for sometime in particular on a flight it is probably safer to have agents at the gate. Why not board the flight? They may be looking in general for suspicious passports rather than just one individual.