As stated, your I-485 was not appovable when you filed it due to your wife not fulfilling the two year HRR. Her application was always going to be denied.
Your options:
obtain a waiver of the HRR (this might not be applicable in all circumstances. It would depend on the country and how exactly her J-1 program was funded).
or
she returns to her country of origin until she has accumulated two years of residency there, then she would be eligible for an IR-1 immigrant visa.
