Everything that was done post-haste, not documented, not version controlled, so on and so on.
To make the project usable, manageable going forward, requires plenty of effort to now redo or improve upon the messy state left from the hackathon.
Certainly I can agree that there are some gains made from the hackathon environment that are lost working in a normal business environment and pace (lets say iterating faster on product while its in infant stages). However, I'm not sure that many of the principles apply after that, when having to continue maintaining and collaborating on a more mature product.