Miracle? Or just cool science?

I have a lot of trouble with what most people call “miracles”. My instinct tells me that everything is explainable. There are no inherent mysteries of the universe. The whole universe operates by a set of rules without exceptions.

When I did physics problems in high school, we ignored friction. Our results mostly matched what we predicted. When I did physics problems in college, we took friction into account and our results matched our predictions a little better. It’s not that friction didn’t exist in one instance and it did in the other. It’s that the more complex the equation, the better we were able to match the results to the predictions. In the 1950s, we discovered a secret nugget of truth in quantum physics. It’s like the friction that I was ignoring in high school. It’s been around this whole time, but we’ve been neglecting it. Now it’s just a matter of integrating it with the existing equations.
Even though quantum physics befuddles us, it’s not magic. It’s not a miracle.
The hydraulic cylinders are broken in my car. If my car was suddenly fixed tomorrow morning, would you assume that it was a miracle or that it was explainable with science? I personally would assume it was explainable with science. Our first hypothesis is often wrong, so it’s important to think of several hypotheses. One hypothesis is that it was a miracle. That’s an option that I can’t deny. But I can’t help but notice these other hypotheses. Such as, could it be, that cold makes the seals rigid in the cylinders and makes a better seal? Could it be, that someone broke into my car, and replaced the hydraulic cylinders? There are probably others, but of these, which is the most likely? I would assume that it’s not a miracle.