A theory...
I just had a thought. I have read about Nathan Fillion being mean to Stana Katic on the set, even going so far as to make her cry.
I have also read that he never wanted Castle and Becket to get together, as he felt the sexual tension they had kept the show going.
However, the writers decided they should get together (for a while, anyway).
So, I'm wondering if maybe he was mean to her in order to keep the tension up, and not because he was a bully.
Any thoughts?