What breed is the doe? And what kind of set up do you have for her? Sometimes things don't go smoothly when first-time does kindle. As a breeder, I employed the "three strikes" rule: three bad kindlings and the doe was culled.
It sounds like she may have had a difficult birth (stillborn kits can be an indicator if the kindling took a long time), and the kits may have been larger than usual. The surviving kit may have accidentally been crushed by the doe, or it could have succumbed to some kind of issue that wasn't obvious.
You didn't see any wounds, right? Some does can become very stressed after giving birth and even kill their own kits; when I first started raising rabbits, I heard a lot about how you shouldn't touch the kits after birth because the doe could kill them, but never had that happen. I generally leave mom and babies alone for the first 24 hours, then check the situation out the next day.
I would conclude, based on the info you provided, that she didn't intentionally harm her kit. She should be better able to care for her babies next time, if you decide to try again. Best of luck!