"All secrets of the nature will never become to mankind, so what's fuss about all this? Anything human brain can't understand should not mean a miracle, or should it?"
The things which do not sometimes come into the scope of science are reckoned sometimes as miracles or sometimes as superstitions. One of my colleagues has recently returned from Japan after having spent couple of years there. According to him, the Japanese who are reckoned as the most educated nation of world have countless superstitions.
As per logic, science is not governing God but it is God who is governing the laws of science. Miracles can be understood as the exercising of special powers of God or Godly people. Prophets like Hazrat Musa and Hazrat Essa were the highly blessed people of God, so they can be believed as exercising the special powers bestowed upon them by God.