I'm no biologist or chemist, but generally plant growth is a huge chain of chemical processes, and if you make some subset of these faster, can it lead, for example, to accumulation of byproducts that are normally used up nearly completely? Or to unexpected regulation of some other reactions, including possibly expressing something bad that's usually only made in the cells we don't eat, up to the anti-herbivore toxins?
Such things cannot be completely excluded, but they should also be easy to detect. I assume that for any such new cultivar many detailed chemical analyses will be done before deciding that all went well.
Such side effects can also happen when using more traditional methods, i.e. selection of improved cultivars from plants that have suffered spontaneous random mutations or random mutations caused by mutagenic agents.
On the other hand, when you insert a foreign gene in the plant genome, e.g. with the purpose of making it pest-resistant, the results are far more unpredictable then in cases like this, where an already existing gene has been duplicated, in order to increase its activity.
