The first reason is, overall record. Clemson (12-1) has a better record than Penn St. (11-2) and Michigan (10-2). Obviously, your overall record is a big factor, otherwise Penn St. would have been in over Ohio St. Two losses seems to be somewhat of a cut line for the committee.
When you get to resume, Clemson beat 4 teams in the final CFP poll. Penn St and Michigan beat 3 each. Washington also beat 4. Then there is strength of schedule. We don't know the actual committee ranking. However, if you look on ESPN's site, Clemson's SOS is #33. Penn St. is 40, Michigan is 54, and Washington is 55. Really, there isn't a reason to leave out Clemson unless you just want to.
You didn't mention this, but I saw that a couple of other posters said the ACC was the worst P5 league. Not true. Here is how the P5 conferences performed this season:
Big Ten
7-4 .636 vs. P5
32-10 .762 Overall
SEC
6-8 .429
42-12 .778
ACC
9-6 .600
42-14 .750
Pac 12
5-5 .500
26-10 .722
Big 12
2-6 .250
19-11 .633
Clearly, the Big 12 was the worst conference. They are the only league below .700 overall, and they were only .250 against P5 teams. The ACC was 3rd overall, and 2nd only to the Big Ten vs. P5 teams, (although they had the most P5 wins).