I would say '没有' is more like an absence of things in which '不是' is used more about identities. for instance, such as when people ask 'do you have a pen?你有一支笔吗' and the negation would be '没有' as for not having such things. or when people ask 'did you have breakfast?你吃早饭了吗？' the answer should be also '没有' because it is also the absence of a thing or activity.However, when someone asks 'Are you a student？你是学生吗？'，then the answer would be '不是'; or if the question is 'Is that a pen?那是一支笔吗?', then you can say '不是'. These two cases are both identities related, either personal identity or material identity. / 'what did you say' in Chinese is '你说了什么？'（ nǐ shuō le shen me)/ Hope I answered your question! I am a Chinese mandarin teacher~feel free to take my class if you want to learn more~