It does so by Scientists allowing for that to be a possible conclusion.
Let's go back to a scientist who witnesses a man walking on water. He investigates the water and finds nothing solid just below the surface that could have supported the man. He investigates the man himself and finds nothing in his bodily make-up (natural bouyancy, etc) which would allow the liquid to have supported him. As much as he is able, he investigates the body of water to discover whether some denizen of the deep could have been floating just beneath the surface for the entire course of the walk and can not find any evidence of any, nor can he hypothesize any. What does he do? Does he conclude that what he saw never happened? What if there are 2, 5, 50, 100 people who saw the same thing? Does he conclude that they were all hypnotized?
Is he forced to avoid the conclusion that he witnessed a miracle? Is that not an option for him?
In order to be honest, the miracle must be an option for him. He should be skeptical of that conclusion, perhaps even more than an atheist. But he must be allowed to conclude it once he has exhausted all else.
Shalom.
The honest problem with your exemplar is that no scientist has observed a man walking on water.