If you say “X is made of Y”, Y is generally a raw material that you can put together to make an X. You can arrange a number of bricks together in a certain way to create a house. You cannot arrange “a beef patty” to make a Whopper. Perhaps you can say “The Whopper is made of beef patty” where “beef patty” (no article) is used as a mass noun. Though as @whiskeychief points out, the Whopper consists of other things as well like a bun and various toppings. I’d probably say “The Whopper is made with a beef patty” - where “with” indicates one of the components of the sandwich.
Also, “The Whopper is made of beef” would be correct because “beef” is a mass noun and it would be understood that you’re talking about the meat part of the sandwich.