Hello. Fault is difficult to put on a situation like this because the true fault is that you are both not communicating properly. It sounds like your wife may be a little bit depressed based on what you said. If she is half hearted into things that she is doing and gets defensive with you, she may be feeling some of her own inner stress that she is dealing with, but she is taking it out on you. You both need to sit down and talk about how you are talking to each other. There is nothing wrong with each of you having your own thoughts and feelings and conveying them, but you have to do so in a manner which is not going to start a fight. When a relationship becomes a competition on who has done what, then the root of the problem must be dealt with before you start thinking about who was right about this part or that part.
When dealing with her studying, think about how the conversation starts and progresses. Is it a simple, "How is your class going?" or are you asking more specifics that someone who isn't happy with what they are doing could take in an over sensitive manner? I would keep those kinds of conversations very basic and general.
It sounds like she is hanging around the house too much and maybe doesn't even realize that she is feeling down about her own life and choices. She may be in a rut.
While it does not sound like you are doing anything wrong based on what you said here, handling this going forward is going to be your choice based on how well you know her. See if you can find out from her how she really feels about life in general right now. Ask her if she is happy. Encourage her to do something else if her classes aren't doing it for her. While you asked about specific things, I think your problem is more of a general nature and that you need to step back and look at more of a bigger picture of things before you can start looking at these details.
There is a deeper problem here other than you going to get her chocolate in response to her making dinner.