This is usually because either:
- The track has become very warped, and combining the tracking and manual roto keyframes on export distorts the shape. Usually the best way to see this is to look at the surface to check if it is severely warping or disappearing.
Solution: Manually roto, or try a tracking with different set of motion parameters. For example if a roto shape is being thrown out by tracking perspective, try only tracking with shear etc.
- Some x-spline points are very close together and are twisting the spline when converting to bezier.
Solution: Delete the offending point. This may take a few goes to find the right point.