Fidelity actually did the right thing - after the fact, they realized that some of the distribution that was rolled over was not eligible for rollover, so they told you about it, and issued two 1099-Rs, one for the non-taxable rollover and one for the portion that was not eligible for rollover, and therefore taxable. When you took the money out from the Schwab IRA, it was a distribution of an ineligible contribution, i.e. an excess contribution. If you told them that, it should have been coded differently; I can't remember the code off the top of my head.
At this point, just report one, keep your records, and be prepared to explain it all.