Notre Dame played 10 power 4 conference teams and the 2 that weren't were Mountain West champ Boise Sttae and Navy that went 7-1 in the American and just missed a chance to play for a playoff birth. ND's schedule was fine, the issue was losing to the 2 best teams it played including 1 it was competing with for a playoff spot..
The bigger issue is ND just dropping down the rankings the last few weeks for no real or apparent reason. I mean in week 14 ND was 9 and Bama was 10. Bama barely beats Auburn and ND beats Stanford by 4+ TD's and yet in week 14 Bama is now 9 and ND is 10. In week 14, BYU was 11 and Miami was 12, which was the same in week 15. Week 16 rankings after Bama and BYU both get absolutely destroyed by top 4 teams, the new rankings have Bama still at 9, Miami now 10, with ND 11 and BYU 12. There is no logical explanation for those 3 weeks of rankings. That is the real issue.