Its hard to say with any certainty what is the cause. The typical reason is related to being too wet or too heavy of a soil mix. Which based on your description was unlikely. There could be other reasons beyond that like a bad cutting (rot was not apparent but was already there), bad cut (not properly callused), and/or seasonal issues (too cool and not during growing season). Sorry but that may be the best I can say. My preference is to start cuttings in the springtime on a heat mat with natural light. IMO light is less important than warmth.

In my experience with root rot, the roots are rotting due to too much water, poor drainage, wet plus cold... In these cases the roots are actually rotting and are mush. What you’ve described sounds like they were in need of a drink to me and it sounds like you’ve provided that. In repotting it’s the same typical advice that you’ve probably seen if you’ve been reading posts on this forum. Growing medium should be well draining. At least half perlite or pumice with the other half being a commercially prepared cactus & succulent mix. That’s a good basic mix that a lot of people use. And of course your pot must have a drainage hole. Not following those two basic things is inviting root rot for sure. If the roots were dry and brittle due to lack of water, they may need time to adjust to their new growing conditions. If they were mine, I wouldn’t water them any more for awhile. At least a couple of weeks. Good luck with them. I don’t know what ruby cactus you mean but aloes are pretty hardy and forgiving provided they have good drainage and proper light.

I'm building a DIY hydroponic rail system that is growing lettuce and I have a resoivor that has a high quality air pump with 4 air stones and a pump. After about 8 weeks of what seemed like a successful system, I lifted my letuce pods and noticed the roots were turning brown which I suspected was root rot. Since I have air stones in my reservior, I do not understand how root rot would happen. At the beginning I noticed I had put too much nutrients in my reservior (900-1000 ppm) for lettuce, but tried to reduce that by adding mroe water over time. Since the lettuce seemed to be doing okay, I did not worry about it. Is it possible this is the cause of my problem or do I need to place my air stones in the rails closer to the plants?

Could you post some photos, especially of the roots and the medium that the orchid is in?