This is a common situation. The rollover contribution made in 2017 is properly reported on your 2017 Form 5498. The IRS has become more aggressive in attempting to find those who report a rollover that never actually occurred, so in this situation the IRS has begun questioning rollovers before the deadline for the financial institution to report the rollover.
Your only recourse in the situation where the IRS questions your reporting of the rollover is to substantiate that you met the 60-day requirement by providing to the IRS account statements showing the date of distribution from the old account and the date of the rollover contribution to the new account. (Hopefully you already did this with regard to your 2015 tax return.)
To avoid this situation in the future, try to complete the rollover in the same calendar year as one in which the distribution occurs.
