First of all, please talk to your daughter about staying on top of the communications she receives from the school. I imagine there were requests for information all along, and she did not pay attention. That is why this has not yet been resolved.
You are correct ... it is her father's info that should be on the FAFSA. There must be some reason they are asking for your info. My guess is that you and your daughter completed a verification worksheet, on which she indicated that her household consists of you & your daughter. It should have been completed using her father, not you. The school would otherwise have no idea she lives with you now, so they wouldn't be asking for your info. I am guessing she completed the form incorrectly and her file has been incomplete all along due to the conflicting information.
Your D needs to visit the financial aid office and explain that she lived with her dad the most ... give them a verification worksheet with her father's household information ... and let them straighten it out.