Joe, Depending on the actual subfloor product, this can be an area for concern, most definitely. When building in potentially wet weather, I like to plastic drape the entire subfloor before walls are up, then cut away the drape after the home is "dried in," but it's too late for that in this instance.
If you're having intermittent rains, about the only thing you can do at this point is sweeping off water as it comes along. If you are having ongoing rain & water is ponding and obviously being absorbed into the decking, you can minimize problems by drilling a 1/4" hole through the subfloor in the low areas to provide drainage.
You will want to watch the flooring carefully for signs of damage such as warping, and discuss what's to be done with your builder. I've seen a builder ignore a 1" in 4' buckle just because of the logistics involved in doing something about it; don't let this happen. Once your home is "dried in" (roof decking and at least felt paper on), keep a close eye on the floors. Good luck