I work as a research assistant for a woman who has a Ph.D., when we first met for my interview she introduced herself as (First Name) and since then I have always referred to her as (First Name) in emails. She has never corrected me or asked that I called her "Dr. (Last Name)" in the three months I have worked for her.
Recently another professor who has a Ph.D. came up in an email who happens to be male and I referred to him as "Dr. (Last Name)" because he has never introduced himself using his first name. Several days later I received an email from my boss asking me why I called him "Dr. (Last Name)" and then she suggested I "look into research on gender bias and the meaning of Dr". She has not directly said I am being biased and maybe I am misconstruing her words.
How should I respond to this? I don't want her to think I am calling her by her first name because she is a woman, but I also don't want to come off as standoffish or confrontational about it.
Edit: I know it is generally advised to wait 24 hours before accepting an answer, but I wanted to make sure I responded to her before the end of the day. I will accept the answer I used as a framework for my response (apology included).