Why dont the present shapes o the continents fit perfectly into a super continent?

Because it has been hundreds of millions of years since the continents actually came to be (through the movement of the tectonic plates). The continents have been eroded so much since then that they won't fit back together perfectly.

Due to the fact that it's been over 300 million years since they have been together. Erosion and climate change over that period of time will have a tendency to change the shape of the continents into an unrecognizable puzzle of landmasses.