Penalties number wise says Louisville played a clean game. The problem wasn't the number of penalties it was when the penalties occurred. Three of the five occurred at key moments. Two were in the red zone and the other was at the end of the game that resulted in more time being ran off.
The key to this team is the OLine. The front loaded schedule is brutal for an inexperienced line. The Auburn DLine is very good. I am not sure if the OLine improved or if Jackson just made them better in the second half. The fumble was going to be a big play, the blocking scheme was good, unfortunately the tackle couldn't get his guy who ended up disrupting the play. They were a couple other plays were the line couldn't get a downfield block.
Overall, missed opportunities in the first half put Louisville in catch up mode against a really good team.