Kenny's explanation is close but his example is not quite right.
We always say "the chickens", in plural, and we usually say "come home" (not "come back").
It's not necessary that the person thought that their action was initially right. For example, when a person uses illegal drugs.
When "the chickens are coming home to roost", the person who has done something wrong is actually paying the price for his or her wrongdoing.
In Kenny's context, the natural choice of words would be:
"Now, the chickens are coming home to roost."