If you transport unfinished wood or an unfinished wooden object through rain or sprinkling, the water drops will raise the grain, and wood stains will show up darker over these spots. The cause is the rough raised grain retaining more of the stain. The accompanying picture shows an example of what can happen.
There are two ways to avoid the spotty staining, both involving sanding (even if the wood has already been sanded). The first is to sand the wood thoroughly to remove the raised grain over the spots. The second is to wipe over all the wood with a wet cloth to wet it everywhere, then sand it smooth.
Because it’s hard to know how much sanding is necessary to cut deep enough to remove all the raised grain over the spots, the second method is actually the safer one because it creates an equal amount of raised grain everywhere. So even if you don’t sand enough to cut through all the water-damaged wood, the staining will still be even, maybe just a little darker.