Heta Quest/WMG

Francis will get poisoned.
A guard mentions he doesn't let people taste his food for poison since he don't want it to get cold. Sounds like Foreshadowing to me...

The masked wizard is Turkey!
I mean look at him! That or he's his unknown evil twin, since in that universe, the canon characters have that are not based on nations.

The jar that Italy got from Gupta? It will
The jar is said to ward off evil, after all.

Arthur's
Well, he certainly seems convinced ? Maybe one of them even is the masked man. (I presume it's, but this could work whatever.)
 * Not to mention Natalya told Alfred to blame the head wizard when she killed him. Does she know about the curse?

Why did Natalya take Feliciano and Alfred's bodies.
I﻿s there anyone suspicious of the fact that both Feliciano and Alfred's bodies were taken away by the villains? There must be planning to do something with them.
 * This Tropette believes that Natalya wants to use them to  Either that, or turn them into Nobodies and send them after the main characters, either way, really.

The stone that made the Green Jewel is the same stone that made the jewel on Malachite's Hand
If this troper recalls correctly, the Green Jewel greatly increases one's magical power and abilities. The jewel on the hand did more or less the same thing, and it's green to boot. Malachite could have found out about the alternate world and the powers of the stones, traveled through dimensions, and got a piece of the green stone to enhance his own magic. And considering the fact that he existed an incredibly long time ago, it was very possible for him to procure it before the stones were destroyed.

Italy, Kiku, and Ludwig are
Actually, Italy would be fine, since  most likely would not effect him as a nation. On the other hand though, Ludwig and Kiku are probably  and, in the beginning of the third part, Italy will have to find a way to

More of the characters will be replaced with nations
Obvious WMG, one or more of the characters will be killed off and their nation counterpart will replace them. .