Okay so I've never really delved into Wes territory before, so someone may have done this already but what if Wes was like... psychic.
He can absolutely glimpse through Phantom's façade into the human boy he was before he died. He has his own little 'ghost sense' and it goes off when Danny gets near him. Like that Scene™️ in JJK:0 where Yuta Okkotsu walks into the classroom and everyone's spider sense goes off.
But it's just Wes who sees it.
It's not like he has some sort of paranoid conspiracy theory, even if everyone in his class treats him like he does. He has legitimate reasons to be suspicious of Danny—the dread that runs up his spine, the cold that comes off Danny in waves, the way, when Wes angles himself just right, he can see Phantom's face writhing beneath Danny's skin—and all Wes can think is, "How is no one fucking seeing this?"
He feels like he's going insane. Everyone treats him like he's going insane. And maybe he is. But even if he was that wouldn't be the worst part about knowing Danny's little secret.
The worst part is that Danny knows Wes thinks he's Phantom. The worst part is that there's a monster in Wes's school and it knows who he is. That seems to love to taunt him, to bat him around in its paws like a cat playing with its terrified food. Danny tosses him smirks when anything about ghosts comes up; Danny stares at him, seemingly purely to unnerve him; Danny crushed Wes's camera with his bare hands while looking Wes directly in the eyes. The evidence just adds up and up and up and all Wes can do is let it happen and try and warn people before it's too late.