Phenotypes are the visually-identifiable or physical expression of genes. Basically, a batch of plants with (virtually) identical genetics can end up looking very different indeed.
I have five Utopia Haze plants on the go, three express the typical Sativa-dominant phenotype I expect - long and skinny, whereas the other two are half the height (squat), and bushy - typical of Indicas.
This could also be due to variation in environmental conditions but I doubt this; light and heat distribution is quite uniform and they have all been on the same diet..
Nonetheless, I am almost certain that these seeds have identical genetics as I obtained them from a reputable supplier and owner of the strain - Barney's Farm. But, as mentioned by the good man above there is substantial in-breeding going on and genetics can become unstable.
In one of those pictures it does look like something was chewing on the leaf, which is strange.
Transplantation induces stress, it could just be the transfer to the new medium causing mild stress while the roots get settled in.
Are you sure there is sufficient Nitrogen? Methinks you can never have too many CFLs!