Genetic anomalies happen all the time, which explains tailbones that usually disappear within weeks of birth (my sister is an example of this as she was born with a tail and covered in hair); as are cases where children are born covered with hair, although there is an identified genetic anomaly where the hair remains throughout a person's life. What about the vermiform appendix, which was once thought to be a vestigial organ without any purpose.
The examples you listed don’t establish evolution. So you have fish with vestigial legs in the end you still have a fish. Again you are citing mutations within a species not one species evolving into another species.
As to miracles, they still occur today. There are documented medical miracles classified as such because medical science cannot explain how people are cured of an “incurable” disease.
As to supernatural judgments, what naysayers can do is find a natural explanation so they discount the timing of a natural occurrence such as earthquakes or volcanic activity. Take manna as an example. There is a bush in the Sinai Peninsula that produces an edible product. The miracle is not in the production of a life sustaining material but in the fact enough was produced to sustain a million people for 40 years.
Miracles by definition defy natural explanation.