My first question is, is this particular beta reader an avid reader/writer of YA? If the answer is yes, then I'm inclined to "guess" that for her, it felt too young. Like somehow the voice or story line or what have you, were more of a MG feel, or on the extreme end of that, maybe it was too "edgy" for his/her taste.
I think it's really important when you have beta readers (and personally I have at least 5 for my novels--though not everyone agrees with this an that is fine) that most of them are people who read in your genre. Not all of them, but most of them. I just can't fathom giving my YA paranormal thriller to a beta reader who reads/writes Adult sci-fi. They just won't connect. They won't "get it". However, it can work if you are giving your book to that particular beta reader with a very specific purpose in mind. As I go along in beta readers, I generally ask each one to let me know of anything that isn't working for them (and please tell me if there is anything they do like), but to pay attention to a specific thing as they read: pacing, plot holes, does the voice ever sound inconsistent, any inconsistencies throughout (which sometimes you can miss when doing many revisions
) and that kind of thing. Also, when I think the book is as prepared as it can be, I give it to 1 or 2 more people and ask them to just read and give me their overall opinion about the story. Not only does this make things easier on the beta reader by giving them a clear sense and purpose when approaching your MS, you'll also find that it will be less overwhelming to you regarding feedback. JMO of course and others may totally disagree. That's fine. This is what works for me and what works for me, doesn't work for everyone. Just something to think about and consider.
GL
ETA: Would it be possible to email him/her and just straight up ask them what they meant? Tell them that you've been pondering their comments and trying to figure out how to approach revisions and would like some further insight regarding that part of her comment?