Without a full audit of the transactions involved, it's unlikely that the IRS will detect a rollover in violation of the one-per-year rule or a failure to meet the 60-day deadline, so failing to report the rollover seems the most likely cause of the notice from the IRS. On your 2015 tax return, did you report the rollover of the second distribution? Unless reported as a rollover, the IRS assumes that the distribution fully taxable.
A properly reported rollover of an IRA distribution will be included on Form 1040 line 15a (or Form 1040A line 11a) but excluded from line 15b (or 11b) and showing the word ROLLOVER next to line 15 (or 11).
