1. Low Accuracy : 3D printed mould will not be that accurate i.e very minor feature, surface finish and dimensional accuracy will be less.
2. Higher Part Cost :As Sonal Mehta suggested the parts that you would inject in the mould should be meltable at low temperature, usually these kind of plastic would be costlier that most general purpose engineering plastics.
3. Low Durability :The life of the 3D printed mould itself will be comparatively very less unless 3D printed in Metal.