Uh I had to quickly look at Wikipedia but apparently the reason it’s transcribed with Ph is:

At the time these letters were borrowed, there was no Greek letter that represented /f/: the Greek letter phi ‘Φ’ then represented an aspirated voiceless bilabial plosive /ph/, although in Modern Greek it has come to represent /f/.)

And so out of the various vav variants in the Mediterranean world, the letter F entered the Roman alphabet attached to a sound which the Greeks did not have.

So Greeks pronounced Phi differently from F and somehow someone decided that it should be transcribed as Ph because it sounded different from F. Maybe the Phi symbol just looked like a P.