It's hard to give you much of an answer without a lot more facts. First, if your short sale has been approved and after the fact you are dealing with inspection issues, it could be as you've indicated. The buyer is asking for a contribution toward the roof which is small in relation to the cost of most roofs. As a short seller however it is assumed you are in financial difficulty. While this has to be the case to some degree or the bank would not approve it, the degree of hardship can vary quite a bit. If you've been living in the home without making payments for several months, it may be possible for you to come up with the funds. On the other hand if the issue that put you in financial distress, loss of job, health, marriage, etc hasn't been addressed you may not have the resources.
I guess my simple advice is to understand your options as best you can and do what's best for you. As Kary indicated, an attorney review is a wise thing to consider. While this will cost some money, it's about more than just the $500.00. If you don't already understand the full ramifications of a short sale, foreclosure and Bankruptcy, it would be good to know while you still have options available to you.
One last thought about the roof, offer something. If you can only do $100, make it available and see what the buyers say. In most cases, getting a short sale wrapped up is a major accomplishment and the buyer's may be willing to take what they can rather than start over on another property.
I would suggest though that you ask your agent and if you have not done so already, consult an attorney about whether a short sale is really in your best interests. If it is, $500 seems like a low price to pay. As I mention in the following link, getting the deficiency on a second loan waived is one of the best reasons to do a short sale (assuming no tax impact). You might also want to read the other piece linked which is the reasons to not do a short sale (the "or not" part).