Is there any difference between
Because I feel like you can use any of these sentences at any time to ask:
Where are you?
All three sentences mean where are you from in Chinese. But there are minor differences.
你在哪 (nǐ zài nǎ) can be seen as a shorter form of 你在哪里 (nǐ zài nǎlǐ),and Chinese people don't use this a lot.
你在哪儿 (nǐ zài nǎr) is more commonly used in northern China.
你在哪里 (nǐ zài nǎlǐ) is the standard one to ask "Where are you?"
To summarize this, 你在哪里 is the most commonly used one.
There is no significant difference, but it's like a slang you infuse into while speaking.
哪儿 is like a discourse particle you add at the end, usually mainland Chinese people use it, but for those who have immigrated outside of China, it has lost fashion and people don't speak like that outside of China. It's not wrong or unsophisticated or anything like that, it's simply a way of speaking.
It's like in English you could say Hello how are you, but you can also say what's up dawg? They both mean the same thing, but have their own unique expressions embedded within.
There are already a couple of answers to this question, and I basically agree that the 3 sentences have the same meaning.
But since you asked, I would like to tell you more in detail.
你在哪儿？ is the most used sentence. It would be correct to say
你在哪儿？ for 99% of occasions.
你在哪里？ may have special applications if the speaker gets in a bad mood. For example, the mother yells at her daughter,
你在哪？ 快回家。 Here the mom has no intention to get the answer but criticizes the daughter for not being home. For example, the girl calls her boyfriend who missed the dating again,
你在哪里？ 我等你半天了。that means why you are not here?