"The cook rarely cooks vegetables."
Translation:Der Koch kocht selten Gemüse.
You're correct about the SVO order, but that doesn't say anything about the position of adverbs. The natural position of the adverb (like selten) is next to the verb. And the natural position of the most relevant object to the verb (Gemüse) is toward the end of the sentence. These two tendencies together encourage the word order in Duo's example.
If you want to emphasise selten in a more natural way, see Raisinnoir's suggestion in another comment.
Here is a useful series of longer explanations about word order, if you're interested.