Of course it makes sense. I think I understand her contention maybe a bit more now.
Basically she became close with a pretty cool guy, a compassionate feeler no less, and somewhere in that process she set your tent up in her friendzone, perhaps inadvertently.
Then after some time you approach her romantically and she is genuinely perplexed but also feels awful maybe that you didn't understand fully that you are just a friend. It's possible she really loves you as a friend but its incredibly awkward and uncomfortable to tell such a friend that there is no romantic interest.
This is also probably why she reacted negatively when you questioned her about her feelings. It broke some internal harmony she had with you as a friend in her heart ( perhaps some Fi voodoo thing

)
Sounds like nobody did anything wrong here but you might have to be told directly where you stand and that's uncomfortable for her but after 3 years of friendship I think she should.