Miracles in the Words of the Sages

In the Talmud, stories are presented that actually contradict the laws of nature. Even those who say that certain stories presented are not necessarily miracles but rather a mistake (by the Sages) in looking at them, there are stories that are tangible reality, with only two possibilities: either they were invented, and this does not seem acceptable to me, or they existed. Is the Rabbi's opinion that the Sages meant that these stories occurred in their simple sense?
Examples of resurrection: Rava slaughtered Rav Zira and brought him back to life, Amoraim who created a three-headed calf, and so on.