That is because cannabis is a prolific seed producer.
This is a survival trait. When dealing with well developed strains, you won't see it as much, but it could easily be 1%-5% of surviving seeds that are not homogeneous. The remainder will be a mixture of performers, some more vigorous in those conditions, others less so. In the natural setting, this allows for survival of the gene pool if conditions change in the environment the seeds find themselves germinating in.
In controlled conditions, seed breeders will often select out the most vigorous plants to work with. What is often forgotten, is that those plants are outliers, and may produce a greater percentage of non-homogeneous plants.
Weaklings will never thrive, so if you plan any breeding, cull it.
The degree to which that plant is stunted, I would get rid of it for room, if that is the space you are growing in.