If you are referring to Royal Caribbean's Navigator of the Seas it has received scores of:
All of these are pretty darn good. If you are basing your opinion of the ship not being clean on the CDC report then I think you may be taking things a bit too literally. The CDC inspectors will always find something that can be improved upon.
If you look at the reports of the ships that score 100 there will still be problems found and there are recommendations of corrective actions that need to be taken. Food not stored, properly, cutting boards that need replacing, etc.
Here is a link where you can look at all the CDC reports for all ships that are inspected.
CDC Vessel Sanitation Program
If a ship receives a score below 85 they have to correct it. They are reinspected in 30-45 days and if not corrected they can be stopped from taking passengers onboard in U.S ports.