Example 1

Incorrect: I want cookies but, the store is closed.

Correct: I want cookies, but the store is closed.

Explanation: The comma comes before the but because the two clauses are independent, meaning they can stand alone as their own sentence. This makes the comma necessary.
 

Example 2

Incorrect: My puppy is only a few weeks old but, we picked her up today.

Correct: My puppy is only a few weeks old, but we picked her up today.

Explanation: These are two independent clauses, so we place the comma before the “but.” If there was a dependent clause after the "but," there would be a comma after the "but."