I just had 1300 sq feet of #1 common red oak floor rescreened repolyed and now the floor looks horrible. There are dull mottled spots where ever there was a pit in the floor and at many of the butt joints. The job was done by the company that originally laid and finished the floors and the original job was excellent. The finisher said that the floor must have been cleaned with the wrong kind of cleaner and that it shouldn't have been rescreened and that I should have been told that upfront. I was not told anything of the kind.

What recourse do I have?

ask them to credit you the cost of screen and coat toward a resand. thats about your only option.

Your description of the problem sounds like "wax burn" to me. Could this floor have been waxed at some point between the original finishing and the recoat? Do you have housekeeping staff that may have done this without your knowledge? Have you used nasty things like Mur***'* oil soap on these floors?
These are questions that should have been asked by the flooring contractor prior to taking on the responsibility of recoating your floor.
There are also easily performed tests to determine this if you don't know definitively the correct answer(s).
Not all prospective clients will be upfront about their maintenance history with their floors, for whatever reason (sorta like not telling your doctor about a chest pain you might have and still expecting a proper diagnoses) so I ALWAYS test a floor for contaminants before proceeding with a recoat. If I detect wax or other contaminant, I offer only a resand, or shake hands and say "have a good day".
However, as Kevin says; ask them for a fair price to resand, deducting the cost of the failed recoat. If they did a great job originally, and it is the same crew and ownership of the company; they are obviously capable of doing a fine job for you.

Thanks Kevin and Dennis:

The salesman who came to the house never mentioned anything about cleaning products. The person who actually came to do the screening asked about the M soap thing. I honestly answered that I didn't think it was ever used but didn't know for sure because we have used a number of different house cleaning companies thruout the past 10 years. I then asked if there would be any problems if M soap had been used. The screener said not to worry about it, that he would know immediately when he started screening if the wrong cleaning products had been used and that some additional work might have to be done.

The flooring company offered 1/2 the cost of the screening towards the cost of resanding and refinishing. I asked for the whole cost and they said they'd get back to me. Still waiting.

Thank you both again, we got it worked out as you suggested.