These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Marty Stu: Ben - though that's been toned down, post-reboot.
Values Dissonance: When the response to Penny's Crowning Moment of Awesome above was this, the fans revolted. Some went so far as to consider it a Kick the Dog moment for Lily. Hayes seemed genuinely surprised and even angered by this attitude. Apparently, the taboo against "making a scene" at a church event (the confrontation took place after actual services ended) or talking back to a preacher is so strong in his family and denomination that it never occurred to him that his readers might feel otherwise.
Similarly, we're supposed to find this a deeply-shocking sign that Penny is seriously out of control and on her way to real trouble. You'd think they'd been in flagrante delicto.
They were, on the other hand, practically climbing into each other's pants.
Which may be unacceptable, but it is normal. Readers from outside RH Junior's subculture fall into this trope when asked to see it as a sign of being severely troubled.
This. For context, Ben has been putting large and apparently frivolous charges on a credit card that they'd agreed was only for emergencies.
And now it turns out that Penny is not only a virgin, but she considers any suggestion that she might not be to be both insulting and ridiculous. Unless she's a substance abuser of some kind and we just haven't seen it yet, then we're supposed to buy her as a "troubled teen" - enough so that she needed to be sent to live with her sister in order to get her away from her friends - based on black clothes and a surly attitude.