I think both of the suggested solutions for this sentence might have incorrect English word order:
• Why the train is not stopping now? -- Why is the train not stopping now.
• Why is not the train stopping now? -- Why isn't the train stopping now.
I think the first one is straightforwardly wrong, whereas the second one just feels wrong (although, come to think of it, I think it generally is the case that when you are negating a question with a present continuous verb you always contract to isn't or aren't, but I could well be wrong). Anyway, reported accordingly.