I've found that before on my remodels.....it makes me want to cry when I find them coming out of the slab because there is no way to correct it but to break the concrete out and move the pipes. Adds alot time to the job.
If you do not want to relocate the pipes which would involve a bit of copper pipe work,sure you could box around them.
If the drain needs to be relocated just break the concrete out and cut the trap off. Installa new trap in the proper location. Drains are usually a bit easier to move in this situation than the water pipes.