I don't know anything about green urine being a sign of an ectopic pregnancy, but it *is* a sign of infection. Along with the pain she's having, it's possible she has a urinary tract infection. An ectopic is possible too (who am I to say it isn't?) but my first guess would be an infection.
One way or another, she needs to see a doctor quickly (like, yesterday) to get it checked out. If the baby's in her tube, it will rupture if you wait too long. She could lose that tube, which will affect her future ability to have children. And if it's an infection, it will only get worse without treatment.