You're right

Here are ND's game-by-game face-off stats:

Georgetown: 17/22 (77.3%) - Won 12-7
Bellarmine: 11/20 (55.0%) - Won 11-6
Detroit: 15/22 (68.2%) - Won 14-5
Maryland: 9/17 (52.9%) - Won 9-4
Denver: 9/21 (42.8%) - Lost 9-8 (OT)
Virginia: 4/18 (22.2%) - Won 8-7 (OT)
Ohio State: 8/21 (38.1%) - Won 9-8
Syracuse: 15/27 (55.6%) - Won 17-7
Duke: 7/18 (38.9%) - Won 8-6
Marquette: 13/18 (72.2%) - Won 8-7 (OT)
North Carolina: 16/35 (45.7%) - Lost 17-15
Duke (ACC): 5/23 (21.7%) - Lost 10-9 (OT)
Army: 12/24 (50.0%) - Won 13-7
Air Force (NCAA): 17/26 (65.4%) - Won 15-7

As you surmise, ND's face-off performance in its losses was pretty horrible. Likewise for a couple wins against lesser foes (UVa, OSU) that were closer than they should have been. The biggest outliers appear to be the wins over Duke and Marquette. Against Duke, ND got killed at the X yet still won, which suggests that Duke's early exit from the NCAA's probably wasn't a fluke. Against Marquette, ND dominated face-offs yet still had to go to overtime.