Defending A Thesis and Expecting The Worst
I doubt it is so common this late. But certainly it is common enough for setbacks to occur at any time. You learn as you go. Sometimes the lessons aren't happy ones. Research is fundamentally dealing with the unknown and it is difficult to schedule. It is impossible to schedule successful completion, actually.
I suggest that you have some options. Perhaps more than I can think of. But, for example:
You could take your chances and leave it as it is. Your advisor might not be happy and the committee might send you back to work.
You could give it (model updates) your best shot and hope for the best. This makes your advisor happy. Maybe it results in success and maybe in some fallback plan, but you can't know that now.
You could, perhaps, just reschedule your defense for a future date to give yourself time to get to a better result. For a doctoral thesis this would be the necessary option in most cases, I think. Perhaps less viable for a masters.
My own sense is that it is important to keep the advisor happy as they are an important part of your future success.