I hope you're not feeling too conflicted! If they're willing to give you credit and a job for something that you consider subpar, then I'm sure you'll really impress them during your internship.
That impulse can be good when it drives you to work harder and improve yourself, but you shouldn't be so afraid to admit that you earned something. You might see flaws in the simulation you submitted, but the professor considered it good enough to offer you a research position based entirely on a single piece of submitted work. Maybe that's more common than I thought, but it seems incredible to me, and you've certainly earned the right to pat yourself on the back! I'm sure you've heard of the Impostor Syndrome. Give yourself credit where credit is due.