I wonder sometimes if this happens when the writer's subconscious lets something loose, what had been restrained by the more natural, habitual main character. Maybe I'm reflecting on my own work, how in one of my novels a character came about unexpectedly and ended up running the show, though he was never the main character. I remember at a reading once an author said, well of course she loved such and such the most too, just as the readers did, because that character was who she'd like to be, but the main character was who she was.

Now, I have to think about your question a bit longer, think about what side characters I fell for (well, obviously, in the book I'd just read, the antagonist is the one who stole my heart). But I'm sure there's more. So, who came to mind for you?