One possible avenue is that Jerome is hearing a difference in the original Hebrew/Aramaic. In Hebrew, Arphaxad is spelled אַרְפַּכְשַׁד. The פַּ has a dagesh, which means that it is pronounced as a bilabial plosive, p. With Judith, Jerome says he is translating from "Chaldean" (i.e. Aramaic), not Greek. So it doesn't matter then what the Greek is doing; if the Aramaic preserved the plosive /p/ for Arpaxad and the fricative /f/ for Holofernes, that's likely what Jerome followed, at least as best as he understood it.
Possibly too he knew the name before his translation from other sources, as Draconis mentioned. The standard way of writing it in Latin would have been to follow the Greek transcription of Olophernes (same name, different person), so it is uncertain from the evidence available why he would have chosen to forego the -ph- and write -f- instead.
Jerome is not entirely consistent in his transliteration, at least not regards with the Masoretic vocalization. In the name Ephraim, Jerome spells it with a -ph- even though the peh lacks the dagesh, yet he spells the name Phineas (which has a dagash) with an F-, Finees. There is no distinction between phi /ph/ and phi /f/ that Jerome would have been hearing, so it is again unknown why he chose to transliterate certain words one way and others another way.
Interestingly, this is not restricted to Hebrew names. In the Prologus, he writes the name Xenofontis, whereas it's unambiguously Xenophontis in Classical sources. I suppose to be thorough one would have to check the apparatus criticus of enough of those references to see if, when, and where there was variation, but at least in the UBS edition, there is no mention of Xenohpontis in the manuscripts.
So, even if Draconis' answer might be technically correct (although we can't be sure), it doesn't explain Finees or Ofni v. Ephraim, especially since in some places the latter is spelled Efraim. Possibly some of it comes from Old Latin, possibly some from the Greek v. historical texts, possibly from learned sermons of the day, but in the end it doesn't look very consistent to me.
Which is funny, of course, since you can also find Holophernes and Holofernes in English papers and books, sometimes interchangeably by the same author.
Short answer is: We just don't know, but it is consistent with Jerome's inconsistency. And at the end of the day, it just might come down to only to inconsistencies.