I have no issues with Rafael being angry and resentful towards Jane but ultimately staying silent about those feelings and his 5-year-old picking it up and acting out on it. Children do that, and Mateo now is in very difficult situation he's unable to control or process properly, since he, you know, 5-year-old, and the grown-ups decide everything without him (while being weak and fallible human beings, even though Mateo thinks of them as almost gods).
I liked that Jane was acting like a child through out the episode, actually mirroring Mateo's behavior and trying to put her own decisions and not very mature behavior on her small child.
I adored Rafael's scene with Mateo and the fact that he was horrified to find out his resentment towards Jane is actually leaking to outside world to his small child.
Rafael is so incredibly depressed right now, and I feel for him a lot. He really doesn't have anyone else in his corner right now. Jane has her entire family, Michael (who also has Jane, his mother, his family), her teacher, Petra, whoever. Rafael only has Mateo now. I don't think he values himself enough to find inner strength through self-love or whatever. He tries to connect but in the end? He's all alone.
On the flip side? The Jane and the glowing unicorn on the porch thing is cut to the Rafael and the stuffed unicorn in the kitchen thing.