pen registers require an application to obtain the set of ip addresses that visit a website and other data from a 3rd party server etc., and are generally considered obtaining the data of the 3rd party and not information that belongs to the entity who is the reason for the pen register. a basic rule is that if the government were to physically do what the pen register represents doing, would it be a violation of the 4th amendment.
example 1: it is not unlawful to go to a grocery store and ask the grocery store for a copy of their security camera so that every face of each person entering the front door can be viewed.
example 2: gps data from cell tower data triangulated is tantamount to following physically right behind a car in which is riding a passenger using a cell phone. this would violate the 4th amendment.