When the scientists looked at the north magnetic poles of rocks that formed at the same time but on different continents, they found that they pointed to different north magnetic poles. The north magnetic poles on different continents wandered over different paths.
If the continents were stationary then there had to have been a different north magnetic pole for each continent for all of geologic time until the present. Since there is no evidence that there were ever multiple north poles, the scientists concluded that the magnetic pole has remained in place and the continents have moved. As verification of this idea, a reconstruction of the movements of the continents that make up Pangaea places the North Pole in its current spot.
Scientists named this phenomenon apparent polar wander because the pole was stationary and only appeared to move.