Learn Italian: Perché arriva in ritardo, dottore? - Why do you arrive late, doctor?

Because we are speaking to a professional like a doctor, we use the formal "you" (Lei). In Italian, the formal "you" uses the exact same verb forms as "he" and "she" (lui and lei). If you were talking to a friend, you would use the informal "you" and ask Perché arrivi in ritardo?

Why do we say in ritardo instead of just ritardo for "late"?

The word ritardo is actually a noun meaning "delay". To describe someone or something as being "late", Italians use the phrase in ritardo (literally "in delay"). Therefore, arriva in ritardo literally means "arrives in delay".

Where is the word for "you" in this sentence?

In Italian, you usually leave out subject pronouns like "I" or "you" because the verb ending already tells you who is acting. The formal verb form arriva plus the title dottore makes it clear enough. You could say Perché Lei arriva in ritardo, but dropping Lei is much more common and sounds natural.