Generally we don't need commas to separate a simple list of 2 things with conjunctions. It doesn't matter whether it's a simple conjunction (e.g. "and") or a complex conjunction structure (e.g. "not only__ but also__")
I like pomegranates and figs.
I like not only pomegranates but also figs.

It's likely that when you noticed commas before the "but," it was in 1 of 2 cases:
1. it was a parallel list of independent clauses, or
2. the comma was actually separating a non-essential modifier, and was irrelevant to the NOT ONLY / BUT ALSO structure.

1. Independent clauses - these require a comma before the conjunction:
I bought a pomegranate, and I plan to eat it today.
Not only are pomegranates hard to peel, but also they can be hard to eat without staining your hands.
(That last example is technically grammatically correct, but awkward. The GMAT tends not to use "not only / but also" this way with lists of clauses).

2. Commas separating modifiers - this is probably what you've seen in most cases. Consider:
I like pomegranates, which are hard to eat ,and figs, which are less so.
Pomegranates are not only nutritious, providing a wealth of antioxidants, but also flavorful.

Generally speaking, you don't have to worry about commas on the GMAT. If you have a keen understanding of comma usage, it can help you to notice lists, modifiers, clauses, etc.
But you don't have to worry about eliminating answer choices solely based on whether a comma should or shouldn't be there!

Hope this helps!