Firstly you need to determine what caused the flowering plant to grow intersex parts. Plants can carry a genetic tendency to easily turn intersex but that does not mean that it is a guarantee. No different to humans whose parents had cancer. That does not guarantee that they will get cancer, however if they find themselves in the same environmental conditions as their parents then the chances of those environmental conditions triggering cancer go up exponentially.
The usual culprits for intersexing is not so much genetics but pretty much always environmental, continued light shocks from light leaks or changing the light cycle, disturbing sleep etc, combinations of other irregularities like over nutrient, too hot when lights on, too cold when lights out, etc. If you can figure out what those triggers were, and don't repeat them with the clones then you should be fine.
