I had a male and female together for a long time. They had 3 successful litters of 2, but after that, the male started killing the joeys. The first time there were 2 in the pouch, then they were gone one day. The next time I changed the pouches, I found 2 tiny skulls. The next time they got pregnant, there were 2 in the pouch, then one day there was just 1 and the other had her tail chewed down. I separated the male, and that joey finished growing just fine.
I don't know why he suddenly began infanticide, but in my experience, I think it would be a good idea to keep the male away while the joeys are still in the pouch. Once they OoP, it should be fine to keep them together.