Translation:Where are you in the afternoon?
This hits on the ambiguity of timing in Chinese. It seems more intuitive you would ask, "Where were you this afternoon?" than "Where are you in the afternoon?" Especially since the latter would be more appropriately stated as: "Where will you be in the afternoon?"
You are correct that the exact meaning of the phrase is ambiguous. Therefore, the intended meaning will depend on the context in which it's said.
Not "were" because it is not a past sentence. "Will be" on the other hand suits fine. If you ask "where are you?", the "afternoon" part is not needed, so this one is either past or future. Since it doesn't indicate past, future it is.
The way this is written in Chinese, is there a way to differentiate between habitual action versus something happening in a particular moment? "Where are you in the afternoons?" (plural, denoting habitual behavior) is not accepted, but I don't know why.
"Where will you be this afternoon" was marked as incorrect but should be correct
This was also my answer, I would like to know from a definitive source if it is acceptable.