Lots of people here much more knowledgeable than I, but from what I've picked up it may have to do with water. I use a moisture meter everyday, but then again, this might not be your problem. Might not even be a problem.
I dont to much about cloning and what not. but If the clones where cut off the mother and the mother turned hermie. Then theres a pretty good chance that all the clones will too. I maybe wrong. But i was thinking, if the clones where cut before the mother turned to a hermie. then maybe they wont turn. and just stay full females. Im not to sure. but goodluck broski.
If the herm. pollinated itself then you would have "femenized" seeds. These seeds have a very high probability that they will be female, but with that you also have an increased chance of herms. as well. Clones cut from a herm will be herms. as they are exact copies of the mother plant.
As for the red stems, sometimes it is genetic trait and sometimes it is a lack of the macronutrient phophorus. If it is the former then theres nothing to worry about and the latter can be corrected with some ferts. high in phosphorus. If the plants are otherwise healthy I would lean more towards the genetic trait argument because phosphrus deficiency can cause other problems like stunted growth and poor flowering.
red stems, ive seen this 3 years in a row in some of my plants, only in the sativa, but ive determined that the ones with red stem, are the ones that have grown the biggest, and (not saying this is a rule) but have always been female for me.
this isnt some sort of small exception, but last year out of the 12 sativa i grew, i got 4 small seedlings showing red colourations on them at early stages and as they grew taller the colouration went from being only in the stems to being around the early fan leaves, this disappearing for a few weeks, and reappearing at a different place in most of these plants, and finally flourishing with a little red around the cola buds.
i only got 4 females from those sativa that year, and no shit they were all the ones that had subtle red colourations, no others.
see how you go mate, make sure to let us know if you notice this phenomena when you determine the sex of your plants, but as far as im concerned its probably a good sign.