Contractor1 and ReliableAmericanRoof pretty much covered it. If you are talking gentle waves "travelling" sideways across the roof spaced the same as the roof joists (high spots over the joists, low point in the wave between) then the problem is sheathing that has gotten wet and deformed, pieces only one joist wide (no pieces should be less than 2 joists coverage), or possibly excessively thin sheathing - i.e 1/4 inch or 3/8 inch (yes, I have seen builders try this) versus what code requires in your area which could be from 15/32 to 3/4 inch thick. However, if this is the problem than the existing roof would have shown the same waves - it would be god for your case if you had recent photos of the roof proving this was not the case.
As Contractor1 said, ripples, like on a pond, can be due to improper stapling or nailing direction (always staple felt and nail shingles moving forward, i.e. in the direction you are laying).
The most common reason I have seen is rolling out wet felt or letting it get wet from rain or dew and not drying fully before shingling over it. When felt gets wet it swells quite a bit, so if it has been stapled and then gets wet it will ripple and sometimes even form folds.
The same effect can happen if the rolls of felt were stacked on their sides (particularly for a long time or in the sun) rather than upright, causing the rolls to become oblong rather than round. Then when they roll them out on the roof, if they do not stretch the felt or "squeegee" it out with a broom or roller, the loosely rolled felt will have "waves" in it - varying in spacing from maybe about 18 inches or so for the part that came off a full roll down to just 6 inches or so for the tail end of the roll. This is pretty common, particularly at box stores - most lumber yards know to stack the rolls on end, but a lot of box stores receive the rolls on their sides stacked 6-10 high on a tightly banded pallet, and leave it that way untill sold, so the rolls come out looking like an elephant walked over them.
Rolling out very cold felt and not "running it out", meaning brooming or rolling it forward to stretch it out as you staple it down can also result in ripples when the cold felt expands as it heats up. (It expands, not contracts with heat). This is not anywhere as common as wet felt or oblong roll ripples.
One other possible source would be cheating on the nail pattern - three tab shingles need 4 or 6 nails per shingle (depends on shingle manufactuer warranty requirement, and on dsign wind speed for the area). A shoddy installer will just pop a nail near each end - saves a LOT of money for the contractor in nails and labor cost. However, shingles will bulge up and tear off easier in the wind, and when they heat up can bulge up in the center. This would create a pettern of little ripples with each shingle bulging up (at least in the sun), rather than large waves. Spot checking the nailing would prove or eliminate this cause.
The end result,unless it is caused by sheathing problems, is you have a problem of defective workmanship. The ripples will provide spots for the wind to get under and teat shingles off easier, make it easier for any ice damming or wind blown rain to get up under the shingles, and make them MUCH more susceptible to cracking due to sunn exposure and to any walking on them. I hate to say it, but this job should be torn off and redone from scratch. The materials hsould NOT be reused, partly because they are now damaged, and also because shingles are almost impossible to remove without damaging them, and they will have holes in them from the original nailing.
If he does not agree to do the repair AT NO ADDITIONAL CHARGE, you may end up having to make a claim against his bond company, see if the city/state will threaten his license if he does not redo the job right, or sue the contractor. Now is the time to get GOOD documentation with camera and a written and photographic report by a qualified building inspector or architect. Your local government may have a building inspector who can document it also, and write up the job as failing to meet code, and therefore having to be redone. I would start with this route if the contractor does not agree to fix it up front.