It looks like you have a "pot inside a pot" set-up. Make sure the inner pot is never sitting with water underneath it in the outer pot or saucer.
It also looks to me like your potting mix is very rich with water-retaining organic material. Jade plants are succulents, they do better with a very fast-draining, gritty mix. I use a commercial cactus mix, then add even more gravel, pumice, or washed large perlite.
The pot they're in is equally important. It should have lots of drainage holes and not tend to retain water. Again, never leave the pot sitting in water.
With a fast draining pot and planting mix the roots will dry out faster, get plenty of air, and be less susceptible to rot.
Yes, that one stem looks like it's starting to rot, that's not good for long-term plant health! I suspect these were four tiny cuttings stuck in a pot, I don't think that one is rooting well.
Jade plants can take a lot of indoor light, a brighter window might be better.
Just some suggestions, I'm sure you'll hear from others too. Welcome to the forum!