it was haley. i think mark sagte it on the special features somewhere, but even if he didn't, it's still haley. nathan & haley have unprotected sex in 3x9. Von 3x11 haley is on birth control, which is the first episode keith comes back. keith & karen don't have sex until 3x13, even if they had before we see it, it still wouldn't have been before haley. karen has lily first because she went into premature labor, which is why dan sagte that she could be having a miscarriage.
karen got pregnant in 3.13 and haley got pregnant in 3.19 both karen and haley had their Babys early karen had something that gives her seizures and haley got ran over and they both had complications karen had her baby at 8 months haley had her baby at six months so karen got pregnant first