How did you come to school?- It's mean that " douyatte" どうやってきましたか？For example by bus, bicycle, by car and so on. But sometimes young people use short cut Japanese.when you heard this sentences , maybe they said " nanide" not "nande". Nanide means How, but Nande means why.I think they asked you "nanide". But if you cannot understand ,please ask them don't be shy. Japanese speak fast most of time, especially young people are!! please keep on learning Japanese^^

It's obvious from context.

As kanae-san pointed, "nanide" means "how". If you break it up, "nani" is a question word "what" , and "de" is a particle "by means of".The pronunciation of "nanide" is often reduced to "nande" in conversation. Coincidentally, there is another question word "nande" that means "why". We just know which one the question is by context, intonation etc.

「何で」という言葉は、友達の間などかしこまらない間柄において通用する言葉です。どのようにして」と「どうして」の2つの意味があることから間違えて答える可能性もありますが、この場合は学校に来る目的は勉強するためだということが明らかなため、どのように学校に来るかを質問されたととらえるのが自然です。何で学校に来ますか？という質問には、意味が２通りありますので、回答者に対して混乱させないためには、「どのようにして学校に来ますか？」と「どうして（なぜ）学校に来ますか？」という質問のほうがより親切です。