Since the 2015 tax return was filed after the regular due date, I believe that the 3-year statute of limitations on filing to obtain a refund begins on the actual filing date, not October 15, 2016 (unless the actual filing date was October 15, 2016). For tax returns filed before the regular due date the 3-year statute of limitations begins on the regular filing deadline, generally April 15, because tax returns filed prior to the regular due date are deemed filed on the regular due date; as far as I know there is no equivalent to that for tax returns filed after the regular due date.
Assuming that the above is correct, you would need to know the actual filing date of the 2015 tax return to determine if the statute of limitations for obtaining a refund has expired.
With regard to filing the 2018 tax return, penalties are determined based on the amount of the balance due. If there is a refund due, there will be no penalty if the tax return is filed late.
