So I'm writing a story and I've been referring to one of my characters sometimes by her first name and sometimes by her last name(as in "Ms. Surname"). Additionally, some of the characters call her by a nickname. Is that too confusing for the reader?
If done with clear enough boundaries and done well it should be ok. It's not like this doesn't happen in real life. You get some people that call people by their surname, first name or nickname depending on the relationship to the person. Just make sure if you are writing it from third person – which I assume you are – that you pick one of the methods and stick with it when referring to that character in your narrative. Look at the military as an example. You can often be addressed by rank, first name, surname, nickname, and sometimes a combination of them depending on the situation or who you are talking to etc.
I'd have to agree. Stick with one whenever you're describing someone in your narrative, but have at it when it comes to dialogue.