If it's new construction... Maybe everything's still loose
I just repoured my basement slab and had a plumber do roughin's for a basement bathroom. The 3" pipe and toilet flange come out of the floor almost a foot. This was done intentionally as neither the pipe nor the flange is glued. Once we have installed the flooring, I'll lift out the pipe, cut it to size and replace the flange at the finished floor level.
Have you checked to see if the flange is glued down. You may find that it can be wiggled out along with the pipe.
Jason