If you for example took the "laws of nature" as it was supposed 1000 years ago or even 100 years ago or even 5 years ago you would have to agree that Scientist find miracles everyday.
The Scientific model is constantly broken and reshaped in a desperate attempt to find consistency. Thousands of years down the line we have uncovered more confusion that solutions.
For example: Quantum theory is currently ripping through the current scientific model. Its unravelling at the seams faster than they can tie it up.
At the same time if someone were to walk on water who is to say its against the natural order. Just because its very hard to achieve and the knowledge of how to do it is unexplainable is no grounds to call it contradictory.
I'm not too sure what you're trying to say. Do you not think the 'miracles' in the bible are miracles then? Or just a lack of scientific knowledge of that specific age?