One problem I have seen (not sure if it ever happens very often though):
Nebraska scores a TD.
<commercial break>
Nebraska kicks off
<commercial break>
Opponent runs first play.
Why would you place a commercial break after a kickoff when you just had a commercial break? I know I have seen it at least one time... but honestly haven't paid much attention to it.
It is even in the rules that they can do it (Wiki):
College football requires twenty commercial breaks per game, with ten in each half. (Exceptions to this are overtime periods, which have none.) These breaks run either a minute, or two minutes in length. Of the ten commercial breaks per half, two are mandatory: at the end of the first and third quarter.
The remaining eight breaks are optional. The timeouts can be applied after field goal tries, conversion attempts for both one and two points following TDs, changes in possession either by punts or turnovers, and kickoffs (except for the ones that start each half, or are within the last five minutes).
The breaks are also called during stoppages due to injury, instant replay challenges, when either of the participating teams uses one of its set of timeouts, and if the network needs to catch up on its commercial advertisement schedule.
What surprises me is that they must be either a minute or two minutes in length. Sometimes they feel like 3 to 5 minutes.