Dear Anshul,
you are using the output pin in a wrong way. You have to rotate them by 180°.
On the other hand, MagCAD can work with very complex circuits, up to 10000 element on more than 10 layers, so don’t worry 😉
Looking at your screenshot it seems ok.
If any error is present the log file will tell you where to look in order to find it.
Best regards,
Umberto