Thank you for being kind in saying the puzzle gave you problems as well.
The arrabiata/$10.99 contradiction I found was that whoever ordered arrabiata ordered capellini, and the person who ordered capellini cannot be the person who paid $10.99 because Nathaniel paid one dollar more than that person according to clue 4, and no one paid more than $10.99. Therefore, since arrabiata = capellini, and capellini /= $10.99, arrabiata /= $10.99. I spell this out not to insult your intelligence but to confirm my own hypothesis. I assure you this puzzle reduced the trust in my own logical ability immensely.
Concerning your other note, I was unsure whether I should follow exactly the grammar in clue 6. The phrase "was the runner" seemed to indicate that the first two conditions only applied to one person. Otherwise, the phrase would be "were the runners." I assumed, very possibly incorrectly, that this was simply a limitation of the program which generates these puzzles, and decided against further speculation. I understood clue 6 to say "The runner who ordered fusilli did not spend $10.99, nor chose marinara sauce." From this interpretation (which, again, may be entirely misguided), I'm unsure as to how the person who spent $10.99 could not have chosen marinara sauce. However, using that information, I solved the puzzle to your answer, and received
"You solved the puzzle correctly in 1 day, 10 hours, 16 minutes, 3 seconds. That's worth 10 points!" (which, if I am able to understand my error, will be the most valuable 10 points I've ever received from this site).
I fear I am missing something, as clearly your solution worked, but I am ignorant of how you achieved it given clue 6. I also readily admit that it may have nothing to do with grammar, and I am simply monumentally missing the point. Any clarification to this effect would be appreciated.
Also, thanks for your explanation and for taking the time to answer.