The hardest part is the transition between "this is just for a paper" and "we're really going to use this."
If you know that the code will only be for a paper, fine, take short cuts. Hardcode everything you can. Don't waste time on extensive validation if the programmer is the only one who will ever run the code. Etc. The problem is when someone says "Great! Now let's use this for real" or "Now let's use it for this entirely different scenario than what it was developed and tested for."
A related challenge is having to explain why the software isn't ready for prime time even though it obviously works, i.e. it's prototype quality and not production quality. What do you mean you need to rewrite it?
