Eh--referees make decisions on every play whether to make or not make a call. A decision not to throw the flag on what is a clear foul to everyone who sees it is a bad call.
Anyway, curious what some of the more flagrantly bad calls are that people remember? Here are a bunch, some of which are more controversial than others...
1) 5th down. I mean, seriously.
2) Oklahoma @ Oregon 2006: the onside kick debacle.
3) Charles White fumble going into the end zone in the 1979 Rose Bowl.
4) "Phantom Clip" in the 1991 Orange Bowl negates game-winning Ismail return.
5) Pass Interference, 2003 Fiesta Bowl. Maybe there was a hold?
6) Miami's "fumble" in the 4th quarter of Catholics vs. Convicts
7) Replay officials overrule ND's Grimes catch at Stanford (2007)
8) Stanford-Cal, "The band is on the field:" Cal player was down; same thing, but more egregious occurred in Miami v. Duke, 2015.
9) Nebraska beats Missouri on the kicked ball (1997) -- any player in that position is going to intentionally kick the ball to try to keep it alive.
Clock issues...
10) 2005 Penn State at Michigan: how much time is on the clock?
11) Wisconsin at Arizona State: officials don't move ASU players off the pile to set the play, allows time to expire. Contrast that with:
12) 2001 Michigan at Michigan State: "Clock-gate"
And some other questionable referee moments.
13) BYU at Washington, 2008, Locker flagged for "celebration" leads to (blocked) 35-yard PAT attempt.
14) I feel like there have been a couple of MSU/Notre Dame games in which Notre Dame benefited from some pretty bad calls. 2013's parade of pass interference calls comes to mind.
15) Nebraska at Penn State, 1982: PSU's receiver clearly out of bounds when making catch, leads to game winning score. And the next year...
16) Alabama at Penn State (1983) Alabama's game-winning TD taken away by referee's call that receiver caught it out of bounds.
17) Syracuse forces overtime against Toledo on PAT that went wide; Syracuse wins in OT (2011).
18) 2008 Hawaii at Fresno State, "running into the kicker" (Sparty, if you want to see an egregious one of these...)
19) 2018 Michigan at Northwestern: "how in the world is that holding?" Or, if you prefer, the "Penalty from Mars."
20) 2018 national championship: Georgia's blocked punt taken away on a phantom offside.
21) 2015 Northwestern at Wisconsin: the referees overturn three Wisconsin touchdowns, two of which were at least highly questionable (the punt return and the pass ruled incomplete).