Hi there,
To me, it sounds like she is hungry since she is taking a full feed. There is a growth spurt for many babies around the three month mark, and since she hasn't been feeding well during the day for a week or so, that might be part of the problem too. I would go ahead and keep things the same, trying to get as much into her during the day as you can. Then, if she is still waking when you know she is getting what she needs during the day you can work on eliminating the feeds at night.
Does that make sense?