Definition from Wiktionary, the free dictionary
Probably from "how comes/came it that" (how does/did it happen that)
- (idiomatic, informal) Why; why is it; for what reason or purpose?
- How come you didn't leave when you had the chance?
"How come" differs from "why" in that the word order of the question is the same as that of a statement. Compare:
- You didn't leave. (statement)
- How come you didn't leave?
- Why didn't you leave?