Is “how come” used outside of the US in England, Australia, NZ?
And how come one has to switch the “you” and “didn’t” in this and similar questions?
How come you didn’t leave?
Why didn’t you leave?
It’s always been my impression that the phrase is a shortened version of 'How has it come to be’….
In other words, ‘How has it come to be that you didn’t leave?’.
used frequently in Aus and NZ. It can be used as a standalone question /sentence or as part of a larger sentence.
Person 1: I have t go back to the shops
Person 2: how come?
etc
It is used that way in the U.S. as well. I guess they are the same at least for those three countries. Being a native American English speaker, I never really though about it but it is an odd phrase when you look at the constituent words.
Some black Southerners substitute “why come” for “how come”. It isn’t that common but some of my high school classmates used that phrasing. It never sounded correct to me but, then again, “how come” doesn’t make a lot of intuitive sense either unless you are familiar with the phrase.
To answer the second question: So-called wh-words generally invert the word order so the second phrase just follows that rule. As for the first, it seems to me that “you didn’t leave” is simply a subordinate clause and follows the standard rule for such clauses, no wh-word there to invert it. Incidentally, the wh-words are what, when, who, why, and how. (Well, how has a w and an h; more to the point it obeys the rules.)
I can’t find an authoritative source for the origin of the phrase “how come,” but some websites say that the first use of it in print was in 1848 in an American publication.
I always assumed that there was an implied verb there — How [did it] come [to pass that] you didn’t leave? — or something like that.
The online OED gives it.
Used in the UK too. I assumed that it was an American import but it seems that it actually came home…
An excuse for a link to the late great (British) Ronnie Laine singing How Come 
The phrase is very common in the UK.
I understand it to mean something more than just “why?” - somehow it conveys a certain surprise, as though whatever it is that’s to be explained is unexpected or unusual, or that the interlocutor should have been doing something else.
When I was in 3rd or 4th grade, my homeroom teacher (who taught us reading and writing BTW) was an older than dirt black lady that used the term: “Why come?” all the time. I told my mom this (mainly because I picked up the term myself and my mom kept trying to correct me on it) and she absolutely would NOT believe me.
I also remember rural Southern Whites using ‘why come’ back in the day, but I haven’t heard it in many years.
It’s also much softer, less interrogative. If someone says they can’t come to your party, saying “that’s OK. How come?” is much more likely to be well-received than “that’s OK. Why?”
That makes it a very useful phrase to learn but almost every EFL student I’ve ever taught has not been told it till I tell them. It is, however, very common in British English.
It’s one of a group of older phrases like wherefore, whence, etc, that are less used these days. Their lineage goes back to Germanic roots, which uses the structure of question word plus normal statement order (at least for those types of words). The question structures in English that use “did” and a change of word order hark back to old British languages which didn’t have as much in the way of case markers so used word order instead. Also, when “did,” “could” and other modal verbs are used, they do all the heavy lifting when it comes to changing tense, so the other verbs stay as infinitives.