The NRCA (National Roofing Contractors and Manufacturers Association) Roofing Manuals, Construction Specifications Institute, standard federal construction standards from various agencies, and InternationResidential Building Code (used by most states) all prohibit placing either the water barrier membrane or shingles over wet substrate.
The decking (sheathing) should have been tarped and work stopped as soon as it was evident enough rain was going to fall to wet the wood or water barrier (felt). Having wet sheathing covered with tarpaper or membrane will trap the water in the sheathing - very bad practice and contrary to industry standardss for roofing. As the other comment said, with normal exterior rated plywood one wetting, assuming your attic is well enough ventilated to dry the wood out in a few days, is probably not going to cause much damage to the sheathing. OSB is another matter - a lousy material for roofing or exterior sheathing for that matter, in my opinion, because when it gets wet it starts swelling and falling apart much like particle board, just a bit slower, resulting in mildew or mold in it (or rot if it stays wet for extended period of time), and also get rough surfaced as the pieces expand, which can reflect through the shingle roofing and also can cause tearing and perforation of the water resistant membrane when the workers walk on it putting the shingles on.
The felt, if it is wet when the shingles are applied, will invariably bulge and crease if not outright tear under the workers feet (or bulge/crease just by being wet in many cases) which can also reflect through to the shingle surface as bulges and waves. There are several nightmare cases a year or two ago in the Home > Roofing section of Browse Projects about that.
In a 1-2 day reroof this can be a tough situation, because the contractor will say it will all level out over time, and of course by the time you have paid for the job and it becomes obvious it will not level out, his warranty period has gone by or he blames it on the shingles or subsequent weather or whatever. With new construction you have more time to watch it to see if any bulges or waves flatten out as the house is built before final acceptance, but if you do not note the issue to the builder and take issue with wet surface roofing as it is going on (or as soon as you learn of it) and get it on the record that you consider that substandard construction, then if you do end up with a wavy or rippled roof surface it will be way too late to get satisfaction for it.
You also run the risk of manufacturer warranties being voided by the roofing materials being put over wet surfaces, or being applied in the rain.
How aggressively you take this up with the contractor is your call, but it is your house and you are not paying him for substandard work. However, raising this issue this relatively early in the job will also tend to sour the relationship for the rest of the job - not right, but it happens.
This is another instance of shoddy workmanship like you see all the time - probably the reason only about 10-15% of AL listed vendors are recommended, and the rest are considered "stay away from" cases. Issues like this crop up all the time - also pouring concrete without cold/hot weather protection during or when sub-45 or over 95 degree temps are expected within 7 days, houses standing framed without roof or exterior housewrap or siding for many months, window and door rough openings being left unprotected for months, plumbing and electrical and even HVAC equipment going in before houses are "closed in", basements and crawlspaced allowed to fill with water, etc. It is a far cry from the "good old days" when building inspectors actually (usually) did thorough inspections at several stages of the work progress, and most contractors did professional work - these days, you go on a jobsite and your eye is constantly drawn to incorrectly or sloppily done work.
One alternative would be to document it, and get the contractor to include a 1 year WRITTEN no-charge replacement warranty against any distortion, bulging, waves, or other noticeable deformation of the finished roof surface for 1 year from closing date on the house. Then whether it is torn off and done right or they cross their fingers is between the roof sub and the GC.
In summary,as soon as you saw them roofing in the rain, had you known then answer at that time, that would have been the time to call the GC on the issue.