No, they were fine to flower. IMO though, cloning is always better done BEFORE you start flowering.
1 - You throw the clones and the original plants togethere and veg them for another week
2 - Flower the clones. If you labeled properly and flower only the clones, you will know what original plants will turn out male.
3 - Throw the male clones out along with their corresponding plants that are now known as males.
4 - Pick the best original plant of each strain to be the mother.
5 - Put the rest (clones and non-mothers) into flowering.
Cloning before or during flowering is fine; however, I believe it's better done during the Vegetative stage.