I am brazilian and the most common is: "Onde você está?".
It is not wrong, but my friends/relatives never said this phrase in this way to me.
This sentence probably came from the skill intended to teach the difference between "você" and "tu" - there are not many questions of this type.
It is true.
It's possibly also regional, tu is slightly more common in RS.
Right. In the south we would say: "Onde tu tá?"
When it narrates "Onde estas" as a whole, it sounds like "estais". Is that just a bug or is that how I should pronounce this phrase?
I was wondering that also.
Same here! The fact that "Onde estais" is a legitimate Portuguese phrase didn't help either.
I think it should be "Onde tú estás
For the most part, pronouns can be dropped if the verb form makes it clear what is intended. DuoLingo is pretty good about handling this, so "Onde tú estás" would probably be accepted as well.