To be honest, I wouldn't be surprised. Gorilla glass isn't invincible. It's meant to give some leeway for those who do treat they devices carefully. That said, reviewers like these need to keep in mind that there are many factors that can contribute scratches on screens. While Gorilla Glass certainly does not get scratched easily by kitchen knives and blades, it can get scratched by dust. You might think that's impossible, but dust is made up of a lot of different things. There might be a diamond particle in there, who knows? But if you get something that hard and rub it against the Gorilla Glass, it's going to scratch, no questions asked.
I don't think it's the S Pen that scratched their screen, but rather their own carelessness. So to answer you question, is it possible that the S Pen scratched it? Yeah. But likely? Nope.
I don't own a Galaxy Note 10.1 yet, but I just wanted to get this across before people start to freak out about how Gorilla Glass can be scratched.