The PotionData constructor used in org.bukkit.potion.Potion.toItemStack is:

PotionData(PotionType type, boolean extended, boolean upgraded)

but the upgraded & extended arguments are flipped (Potion, line 324)

meta.setBasePotionData(new PotionData(type, level == 2, extended));

changing the above to

meta.setBasePotionData(new PotionData(type, extended, level == 2));

seems to fix the java.lang.IllegalArgumentException: Potion Type is not upgradable (and similar) errors I've been getting since the reworked potions API commits.