This idiom or expression like phrase has to do with:

Telling the truth.

When someone says “Clinton came clean on Monica,” they mean “He told the truth about the Monica incident.”

This idiom or expression is about:

Deserving something.

When someone says “She had it coming,” they mean something like “She deserved it,” or “It was her own fault,” or “She should have expected it,” or “She shouldn’t be complaining,” etc.

We can also say:
It serves her right!