Here is my top 3 for UM
#3 the scholarship scandal at UM from 1973 that lead to a de-emphasis on football at UM, and eventually Swarthout leaving and a lost decade of football at UM.
#2 in 1993 President Dennison led 7 other University presidents in voting to reduce the football scholarship levels from 63 to 45, effectively turning the Big Sky into a D-II league, or as Idaho's John L Smith said, turning football into a club sport. The move finally allowed Idaho and Boise State to convince the board of regents that the Big Sky was a sinking ship filled with Schools that didn't want to compete at the D-I level, and the Idaho Board of regents granted their request to move to I-A and the Big West.
The Big Sky later rescinded the decision in an effort to keep Idaho and Boise State, but too late, once the gate was open those schools were not coming back.
#1 the decisions to de-emphasize athletics from the 1940's to the early 1960's, leading the program to go from the Pacific Coast Conference to Skyline to D-II.
If we include MSU I think a coach dealing meth and players killing each other over cocaine deals going bad has to trump any budget issue or coach firing.