Hi
It could be the rapid acting left over from when she eats, though I believe Novorapid and its ilk only has a duration of about 4 hours. I believe that hypos around the 3am mark are common, possibly we need less insulin at that time of night. Also, if it keeps happening and you cant fathom it, ask for a continous glucose monitor, to get a reading on a 24 hour basis
The other option of course is that the basal is not set right. What kind is she on and what time does she take it?