Why don't the present shapes of the continents fit perfectly into a supercontinent?
The borders (coastlines) of the continents underwent a number of changes since the split. Often, chunks of land were washed away with water, slowly or in bigger portions. The coast was generally "smoothed" by the ocean currents too, and in some places more land was added with the material that the ocean currents brought.
Then, the tectonic plates continue to move, so this adds to the changes of the shape of the continents.