But suddenly everyone, Gabe included, acted as if Ben has been there for years
Should be "had" (past perfect).

"It is starting again!" hissed a Sasha.
Are there more than one?

… but the coffee shop across the street were used to dancers
I’m not sure about this. The plural may be justified (or even required?) in referring to the shop’s staff and patrons rather than the shop itself.

… refusing to say what the hell’s she so scared of
Shouldn’t this be "what the hell she’s so scared of"?

An ice-cold hand punched Cassie it the gut.
Should be "in the gut".

A little dancer will come rushing in an explain it in detail.
Should be "and".

… but her disappearance’d had some unforeseen consequences.
Is this meant to be a contracted "disappearance had had"? If so, it’s technically correct, but still looks weird to me.

Essentially, she was making herself extremely impopular with everyone.
Is "impopular" a valid synonym of "unpopular"? I don’t know, I’m not a native speaker; but MS Word spell check says it isn’t.

The Opera Ghost got to him.
Although "had got" or "had gotten" doesn’t flow as nicely, in the context this should be past perfect.

His story couldn’tend here.
Missing space.

… and the Ghost would have no reason to elliminate him.
Should be "eliminate".

She left Blue’s dressing room to change
Who is Blue? From context, this might be Henry Callot’s dressing room?

… lying on its own at a velvet pillow
I guess you actually mean "on (top of) a velvet pillow", not "at (the side of) a velvet pillow".

… covered most of in in fact
Should be "it".

Cassie searched around it to find what she just assumed ould have to be there.
Do you mean "would have to be there"?

She rejoined them half an hour later, just as the door spung open.
Do you mean "sprung"?

On a dusty throne laid the cape of the Phantom
Should be "lay"; the tenses of "to lay" (active) and "to lie" (passive) are confusing.

"But I was was hoping... "
Cassie may be stuttering here, but I don’t think this is intentional.

Despite not being a Phantom of the Opera fan, I enjoyed the read, and writing up what caught my eye didn’t feel like work.

HG