This may or may not be the case but perhaps, her feelings toward Stefan were influenced by the compulsion when she met Stefan? He was the first adventure, passion, a love that consumed her before she met before Damon [technically].
Obviously, she loves Stefan genuinly but could it be possible that she actually started feeling for him because she was told to get that love she wanted? I feel like the conversation Stefan and Elena have on that walk on the bridge about Matt and Elena's relationship, was a flashback back to Damon and Elena's first meeting. She said her and Matt's relationship didn't have passion. A passion that she felt her and Stefan had. Was that not what Damon had described to her and then told her, he wants her to get everything she wants?
Just thought i'd share. 😆