When I saw your title with the words, "Did you read the directions?" it reminded me of a teacher I had in school, although I think I was older at the time. That instructor's "pet peeve" was to be sure you read ALL the directions and plan for getting your work done. There was one "test" I will never forget, where she handed out a packet with several pages, and said we had X minutes to do it. I was a very good student, but I remember feeling like it would be a lot of work to do in the time we were given. Like most kids, I started to write answers on the first page, but for some reason, I flipped to the back sheet to see how hard the problems were going to get. That's when I saw a sentence at the bottom of the page, which basically said "This is a test to see if you read directions before rushing into the assignment. Do not answer any of the problems, just put your name and date on the top of each sheet, and turn in your paper." I quickly erased whatever answers I'd put on page 1, named and dated them all, and walked up to give it to the teacher. I wasn't the first kid (so obviously others really did read through ALL the directions before starting) but I "got" the message she was trying to drill home.

Having said the above, I DO believe your son's teacher sounds harsh. What I wonder is if she may be holding him to "higher expectations" than other kids in the class, because he normally does excel in his work. Right or wrong, because his work is usually above average, she may have felt he would be emotionally more mature than most other 2nd graders, so she wrote a more critical comment.
I think you could could send her a note, or call her, and just let her know that your son felt badly about the situation, but everyone makes mistakes. Like most young children, he responds better when given positive reinforcement for doing well, and you hope she'll be able to provide that encouragement, too.