WMG / Hatoful Boyfriend

The whole Shuu's flashback in Bad Boys' Love route is a case of Unreliable Narrator.
In reality, when Shuu understood that Dr. Kawara isn't going to answer his feelings, he infected him with a sample of virus he had and, when he was buried, stole his body and explored it most intimately. The whole story told in a flashback was made up by Shuu to make Ryouta even more miserable and break him completely.

Well... that would be very in character. Also, remember that Hiyoko remarks: "Everybirdie knows that even just talking to him can bring you down with supergillus, psittacosis, or even worse things". A clue?

Le Bel's real egg
Yuuya tried to destroy it and he believed he did. In reality, it survived and grown up to become Oko-san

MAJOR SPOILERS FOR BBL AND HOLIDAY STAR: Hitori betrayed the original Kazuaki not because of outright cruelty, but because of his severe psychosis.

After watching his only brother Nagekiís suicide, the traumatized Hitori felt all alone in the world. Additionally, the original Kazuaki also felt all alone in the world through his severe clinical depression. By chance, the two lonely birds met and were drawn to each other through their similar circumstances, as well as the fact that they were of the same species. Just as Hitori was a nurturing older brother figure to the sickly Nageki, he also became one to the emotionally troubled Kazuaki. And even if Kazuaki was clingy and emotionally fragile, Hitori really did care for Kazuaki and found happiness in their friendship.

However, Hitori still had an aching guilt for moving on with his life and befriending Kazuaki at the expense of no longer grieving for his brotherís untimely death. This is where Hitoriís trauma from watching Nagekiís suicide began to manifest into psychosis. A dark hallucination of Nageki would constantly appear to guilt Hitori for having caused his suicide. The hallucination also criticized Hitori for befriending Kazuaki instead of grieving its death. After a while, Hitoriís mind couldnít bear the hallucinationís constant accusations anymore and he began to believe and acquiesce to its ruminations.

The dark Nageki hallucination constantly demanded Hitori to avenge its death. The only way Hitori could accomplish this would be to murder Kazuaki, steal his identity, and then pursue Nagekiís tormentors. The dark hallucination rationalized this by describing Kazuaki as a bother, always complaining and getting in the way. He had to die. It was about time Hitori said goodbye to him. After all, Kazuaki always did talk about wanting to die; Hitori would just help him to it.

This is why Hitori cruelly tricked Kazuaki into suicide despite their growing friendship; he was led into these diabolical actions by the dark Nageki hallucination the whole time. And as Hitori told the dying Kazuaki, even if the world was such an awful place, he still had things to do in it. ~Brussell

Everyone is a psycho or a murderer at some point
Or at least, they have a potential. We already know that Shuu and Kazuaki qualify this. Now let's look at the others :

Ryouta is Brainwashed and Crazy in BBL route.

Nageki commited suicide (tried to pull it again in Holiday Star).

Anghel is confirmed to be a megalomaniac by Moa.

Yuuya is a Stepford Smiler who killed his half-brother when he was one years old.

Okosan is Playing God;.

The protagonist, Hiyoko herself also qualify. Look at her wish list at Tanabata. Conquer the world by force? And by Shuu's route, it's implied she wanted things to happen.

We haven't seen Sakuya acted this way....yet. But there's still the next sequel...

Nageki is originally from America, but his parents were killed there and he moved out as a refugee.
Mourning doves are very common in America, and Hiyoko wonders at one point what Nageki is doing in Japan. Nageki is an America-born mourning dove, and he lived there with his parents until they were killed by humans. The human/bird conflict was much more dire in America than it was in Japan, so Nageki was able to escape as a refugee to Japan, where conflict wasn't as bad as the rest of the world. One of the reasons he started reading books so much was so he could study Japanese and be able to speak the language fluently. He spoke Japanese so often that he forgot his mother tongue, and his terrible time in America became a distant, hazy memory as he learned to love his new family.

Some of the more exotic bird-people are descended from zoo animals.