Sorry for your loss.
Sadly it's impossible to know exactly why... She could've been too stressed as a new mom in a new house, she could've not been producing enough milk, she could have a sore nipple and didn't want the Joey to nurse, there could've been a genetic issue with the Joey that she could sense, it could've been an inbred Joey (if you don't have lineage), she might not have had the nutrition to support two joeys (calcium or protein), or it could be a complete random accident.
Did you ever find the Joey outside of the sleeping pouch, being ignored by mom, or crying and mom not attending to her? What diet is mom on, and has she always been on a good diet? Do your gliders have lineage? Were you weighing the joeys at all, or checking to see if they were hydrated?
Unfortunately we can only speculate. And sadly, this is a common part of breeding...sugar gliders in particular can be brutal with their joeys, it's just natures way.
Keep an eye on the other little girl, weigh her daily if you can, and be ready to pull her if you see signs mom is not caring for her.