Chihaya route is known for containing most plot holes in Rewrite. After a bit of thinking, I could remember about 4 of them, but there’s probably more.
Plot hole 1: Dual wrist blades
Chihaya’s route was the only one where Kotarou could bring Aurora out of both his hands. He just up and made a second wrist blade on his left arm as well, creating dual wrist blades. He shouldn’t be able to do that in the first place because Key’s bow that enables Kotarou to use aurora resides somewhere in his right schoulder or right arm. He can’t make Aurora come out of anywhere else because of it. He tried to and experimented in Kotori’s route but he couldn’t make it happen. And he didn’t rewrite his Aurora specifically to do that in Chihaya’s route. He just formed a wristblade from his left hand in mid-fight like it was totally natural. Similarly, he made a whip out of his aurora, then pulled himself up a tree with it. Again, he tried but failed to do anything similar in Kotori’s route.
Surely, he could do crazy things if he rewrote his Aurora like he did in Akane’s route but he didn’t do that in Chihaya’s route.
Plot hole 2: Midou’s faction
We know that there are two factions in Gaia: Kashima Sakura’s “disciples” and Suzaki’s group. Chihaya, Akane, and even Sakuya refer to the faction Midou belongs to as “extremists”. But as we learn during Akane’s route, the “disciples” are the actual extremists, while Suzaki doesn’t even plan to end the world at all. Chihaya might be ignorant, Akane might have been lying, but Sakuya sure as heck wouldn’t be deceived so easily, or have a reason to lie about Suzaki’s group being “extremists”. So either Midou and his assassin buddies belong to a non-existent third faction, or Tonokawa didn’t know anything about Suzaki’s group and Suzaki, since his name didn’t appear in Chihaya’s route even once.
Plot hole 3: Strongest familiar of Gaia
This matter has never been clarified in the game. Is Sakuya Gaia’s strongest familiar, according to Tonokawa’s routes or is it the earth dragon after all, like all other routes say? They have never both appeared in the same route and Moon is the only route not written by Tonokawa where Sakuya’s existence is ever mentioned.
You could argue that it’s the game’s plot hole, not exclusively that of Chihaya’s route, but since Tonokawa’s routes are the minority, the fault should be lying with them.
Plot hole 4: Midou, the whisperer from hell
Probably the biggest plot hole of Chihaya’s route and the one most deserving of this term. During the final fight against giant Sakuya, Kotarou needed fire to break through some of the thicker vines. Conveniently, Midou starts talking to him from hell, summons Fuego (we can see a normal flame appearing once), which then fuses with Kotarou’s Aurora blade.
So, how did that happen? Even assuming that Midou’s talk from hell is just an illusion of Kotarou’s, a dead man can’t summon familiars and familiars can’t move if all their contractors are dead. Kotarou never made a contract with Fuego and even if he did, while rewriting himself is one thing, usurping a familiars power and fusing it with his own shouldn’t be possible with just rewriting.