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She probably gave birth on the wire floor. One of mine gave birth to one in her loo and one in another corner and the bulk on the other side of the cage -- and this was an experienced doe, I just put it down to random accident.
Or it could be that she fed it and it latched on and if she has sore mammaries, that can be uncomfortable so when they latch they hurt the doe and she wants to leave, check all her belly to make sure there is nothing inflamed or hardened, also look at her nipples to make sure they are all as they should be. Sometimes the kit just doesn't let go and is carried out anyway. Just rebuild the nest and pop it back. You can always take the kits out and return them in the morning and evening for feeding.
If she only had one kit, it may well be that she is at the end of her motherhood years. I have one such doe currently on her very last litter before retirement -- she went from 14 kits to 6 last litter, and this morning she produced only 2. She is 2 years old ad her sister just had 8 babies (down from consistent 10).