Why was a Greek city with the name Mαρωνεια written Marogna in Latin and not Maronia?

As far as I can tell, you are referring to Maroneia in Thrace, and the rendering Marogna appears in Smith’s Dictionary of Greek and Roman Geography (1854)

Maroneia is reckoned among the towns of Macedon. The modern name is Marogna, and it has been the seat of an archbishopric.

Cramer (1828) also gives the name of Marogna (A geographical and historical description of ancient Greece), citing a P. Mela.

I don’t see any evidence for Marogna being Latin; it is an Italian rendering of /maronja/ (Greek Μαρώνεια Bulgarian Мароня), and is presented as modern explicitly. With Italian mariners having the run of the Mediterranean, it would not have been unusual for a port in Greece to have an Italian rendering, or for the early 19th century rendering of a Greek (or Bulgarian) placename to have been spelled via Italian.