Let's start by taking all of the conspiracy theory out of this.  Let's assume that Michigan legitimately deserved that extra second and won that game fair and square. Let's also assume that the Big 10 timing system, normally in sync with the scoreboard (televised) clock, was somehow slightly off on this occasion but that the normal rule of thumb is that the conference timing system trumps all.

If all of the above is true, it doesn't make matters any more acceptable.  This is a day and age where technology decides everything from balls and strikes to tennis line calls.  Cameras let us know whether the receiver got two feet in bounds or whether goaltending should still stand.  There can never, ever be any circumstance where something which we've all witnessed with our eyes (and are in universal agreement over) takes a backseat to anything which completely lacks any transparency.

Back to college sports, I believe we can all agree that if the roles had been reversed, there would simply be no way that Western Michigan would be granted an extra play.  What adds to the outrage is that this was Michigan, one of only a handful of bluebloods who can generate this level of either fandom or animosity.  It doesn't help that Michigan football has been filled with scandals these past few years, some legitimate and some way overblown, including during its national championship season.  Society dictates that we should care far more about the Wolverines than these Broncos.  However, WMU is the defending MAC champion (with practically its whole team back) and a legitimate contender to become the Group of 6 representative in the Playoff.  This outcome has real meaning to WMU as well.

Nevertheless, it's yet another example of why hypothetical Syracuse makes the dance with a 4-11 record in Q1 games while hypothetical Dayton gets left out with its 2-1 record in such games.  Syracuse gets to crow that it won twice as many Q1 games as Dayton (legitimately, with a straight face) and point out that Dayton really needs to upgrade its schedule.  Dayton gets to point out that they tried to schedule 20 Q1 games that did not work out and that nobody would go on the road to play them.

The difference of course is that little guy WMU got to play its game, and for all intents and purposes, win its game.  To all, except in the eyes of the P4 and NCAA decisionmakers whose opinions are really the only ones that matter in the end.