Are you saying that the spokes are coming up though the tops of the nipples and puncturing the tube?

Is the wheel aligned, meaning does the rim wobble or move up and down when the wheel spins? If the wheel is round and aligned, then it's a simple matter for grinding the excess spoke down to the nipple, then covering both with a rim tape to protect the tube. If you don't have an actual rim tape, you can use one or two turns of cloth surgical tape.

The reason I ask about alignment, is that it's rare to see this in a new wheel, and I was wondering if someone attempted alignment by working the nipples.