Review the item:
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.