Take a look at the sentence again:
Sick with the flu, Howard craved a big hot bowl of his grandmother's chicken
soup, but in the refrigerator, Howard had
only a jar of olives and a carton of milk, cream of olive soup, Howard decided,
would only worsen how he felt.
There is no problem with the comma between soup and but. Howard craved a big hot bowl of his grandmother's chicken soup is a main clause. In the refrigerator, Howard had only a jar of olives ... begins another main clause. You can legally connect two main clauses with a comma and a coordinating conjunction like but.
Go back to the sentence to try again.