I've seen many arguments on the pronunciation of Phione.
I personally pronounce it "Feeown." But others say it should be "Fee-own-neh" (like the Japanese pronunciation)
Another is Arceus. I used to pronounce it "Ark-ee-us," now I'll sometimes say that or "Ar-see-us."
I remember when Ruby and Sapphire first came out I pronounced Meditite "Med-it-it-tee" xD And I used to pronounce Pidgeot "Pid-GEE-ot"
I used to pronounce Mismagius "MIS-magus" (it sounds kinda weird when I say it like that xD) until I took a good look at the name. Now I say "Mis-MAG-ius." And I don't think I've ever really said Giratina out loud. I guess it'd be like, "Ji-ra-TEE-na."