He could just be referring specifically to FO troopers flying, not troopers in general. And nothing from the Clone Wars matters because 3P0’s memory was wiped by Bail Organa at the end of RotS.
The only problem I’ve ever had with the line was Finn repeating it as a question, like he wouldn’t know. That implies more heavily than anything that FO jet packs are a very new tech in TROS, which EU lore will probably disagree with at some point. If only 3P0 says the line, I think that’s fine, as I don’t imagine he’s seen the front lines often during his time in the Resistance.
Late to this response but anyway to be fair, Finn worked in sanitation and the impression TFA gives is that he was strictly ground team, it’s very likely that in an organization as large as the First Order is, he could’ve just never heard of it.