Everything is more readily apparent in hindsight or after the fact. As has been noted the reliability of a college kicker is very different than that of the NFL and Toledo's kicker is probably not as good as most top 25 programs and it's early in the season and a very high pressure situation.
Taking a down prior to the end zone is also not without risk. The easiest would be to run out of bounds as one has to worry about a fumble, being stripped, etc. if they are in bounds but it's not always easy to have such situational awareness in the moment.. The fact of the matter is that taking a 4 point lead with less than 2 minutes to go isn't a bad situation to be in, fact ND got the ball back with 1:35 left and no timeouts. Had Toledo been able to make a few stops the game is over.
The other potential downside of taking the down, running down time and kicking a field goal is the kick-off return. A FG by Toledo would have given them a 1 point lead and a field goal by ND would have won it at that point. Again hindsight is 20/20.