When someone was supposed to arrive somewhere at a certain time, but they arrive late, you can ask them "Where have you been?"
A: Where have you been?
B: Sorry, I had some car trouble.
"Where have you been?" usually suggests that you're a little annoyed.
Note that, if you see someone later, after leaving the place where you were supposed to meet, you don't ask "Where have you been?" For example, if your friend missed the yoga class that you usually attend together, you can ask this the next day:
Where were you yesterday?