Which structures specifically? It could be that you are spotting inscriptions put up by later popes, who often commemorated their restoration or movement of ancient monuments. The official Latin title of the pope is Pontifex Maximus, borrowed directly from the Roman emperors, although as you point out it was only one among many titles given to the principes.

Some examples, to help distinguish in future! Here is an inscription on the Colosseum, commemorating restorations by three different popes - Clement X in 1675, Benedict XIV in 1750 and Pius IX in 1852. Compare that to the inscription on the arch of Septimius Severus. Pontifex Maximus is there on the second line, but listed alongside tribunicia potestas, imperator, consul, proconsul and pater patriae.

Of course my assumption might be wrong! If you know of any inscriptions where the emperor is only names as Pontifex Maximus I'd love to see it!