Number 1 reason is because momma isn't producing enough milk. If the mother decides at any time, that she doesn't have the strength raise one or more of the joeys, she will reject/terminate them. Nutrition = Milk
This has been proven to be a myth. If a sugar glider female can and does produce milk the entire time she is carrying a joey in pouch, she does not just stop producing milk.
What causes the mom to stop producing is often times the joeys do not have enough suction to them, which in turn does not allow mom to produce.
If it is the fact that mom, herself, does not produce milk, the joeys never even survive while in her pouch and often times you are not even aware she was with joeys.
Another reason joeys stop eating or why it may seem mom is rejecting is more times than not, mom has mastitis. Although this is not often visible to our eye since moms teats are inside her pouch and its not like we can just open moms pouch to peek inside (in most cases). This has to be determined by a vet
in most cases, and even if you can tell your mom has mastitis she should be put on an antibiotic since it is a bacterial infection.
Another cause of losing joeys is actually the pouch they are in. If you have a normal cage pouch and it is hanging high, years ago we discovered that the joeys get stuck under the weight of mom and dad and actually suffocate. Once the joey loses body heat, the parents no longer acknowledge the joey and dispose of the body most times.