I suspect that your friend misremembered the phrase.
Concerning the actual phrase that Julius Caesar said, the biographers offer conflicting evidence. Suetonius tells us that Caesar died in silence, though he admits the tradition that Caesar said in Greek: "καὶ σὺ τέκνον;" Cassius Dio echoes Suetonius, claiming that the "truest account" says that Caesar was silent although some claim he said the above Greek phrase. Shakespeare famously gives Caesar the words, "Et tu, Brute?" Perhaps he felt that Latin spoken in an English play would have a similar effect to Greek spoken in a Latin context.
Regarding the particular phrase you cite ("Tu quoque, Brutus, mi fili?"), I suspect that it is misquoted, since it returns pretty much 0 results in a web search and it's not good Latin. As you note, the vocative of "Brutus" is "Brute." "Fili mi," however, actually is the correct vocative.
Modified in this way, the phrase "Tu quoque, Brute, mi fili?" does appear to have some currency. For reasons that are utterly opaque to me (if Wikipedia is to be trusted), it appears that different language traditions favor certain versions of Caesar's final words, e.g.:
Despite the title of the Italian article, however, I can find no source that actually ascribes these words (or their Greek equivalent) to Caesar. It seems to be an explanatory gloss.
To summarize: Caesar probably said nothing when he died, but historians mention the account that he said in Greek: "καὶ σὺ τέκνον;" "τέκνον" can mean "child," "young man," or "son," so "fili mi" is a reasonable Latin translation, yielding "Tu quoque, fili mi" or (most literally) "Et tu, fili?" There's no evidence I can find, beyond Shakespeare's dramatization of the incident, that he addressed Brutus by his name.