It depends on the states - in some states the amount in box 16 is bigger than the amount in box 1 for legitimate reasons. Usually it's because the state doesn't exempt certain items from income (for example, HSA contributions in CA and NJ) like the federal does.
However, if that's not the case for your daughter then yes, you can allocate the income based on where she lived at the time it was earned. That can be based on time spent in each state, if she earned her income prorata over the year, or it can be based on her paystubs.
@ytischler
