After the split from the supercontinent, the individual continents underwent a number of changes of their shoreline. For example, the constant flow of water "smoothed" the surface, which meant that in some parts the land decreased (was washed away by the currents) and in other parts the land increased with the accumulation of the material that the currents brought.
This changed the shape of the continents in a way that they no longer "fit" together perfectly.