All those things are completely consistent with reality. Every year there are virgin births[0] (not immaculate conceptions[1], which is a term specific to the birth of the Virgin Mary herself), water turning into wine[2], and people walking on water[3].
I think what you mean is, the specific details of those miracles, as described in the Bible, have not been observed since, and they would have required a succession of extremely improbable quantum events. No one disagrees with the notion that those events were scientifically unlikely, but unlikely events are still consistent with reality.
[0] https://en.wikipedia.org/wiki/Parthenogenesis [1] https://en.wikipedia.org/wiki/Immaculate_Conception [2] https://en.wikipedia.org/wiki/Irrigation [3] https://en.wikipedia.org/wiki/Snowshoe