I asked my Chinese friend a question in Chinese, but she doesn't understand I wanted to ask her if she misses China and her friends in China.

So I asked,

你不想中国和在中国里的朋友吗？

Don't you miss China and your friends in China?

But instead, she understood it as 'I don't miss China and friends inside China'. Where have I gone wrong?
Just sounds odd to natives, 你不想念中国和在中国的朋友吗 is the common expression.
Add 念 to distinguish it from 想(think) and 想(miss).
You don't need 里 after a place name.
But this is still not normally said by the Chinese. The typical question is 你不想念你的家乡/祖国吗? 家乡/祖国 includes friends and other things.