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.
The fact that her public behavior was indistinguishable from girls who WERE sneaking off to dope, smoke, drink, and fornicate, what conclusion should her parents have reached? Only teenagers themselves expect others to see the invisible halo of innocence over their heads.
Her public behavior was indistinguishable from the overwhelming majority of teenagers. Her parents are free to find it unacceptable, but to consider it self-evidently a sign of serious trouble inflicts this trope on most readers.
Perhaps this Christian troper can clarify some things. In a lot of Christian homes and churches, a "surly attitude" is treated as a symptom of a troubled teen. The whole teenage rebellion is not considered a normal part of growing up, and any amount of it is considered a sign that the kid has, at the very least, issues with authority. So, really, the Values Dissonance in this situation lies between the Christian attitude that teenage rebellion, in and of itself, is bad, and the average belief that it's perfectly normal and all teenagers will rebel at some point.
You should be more specific about your denomination. That belief is not shared by all Christians. But yes, that does make this a textbook case of Values Dissonance.
There's also the issues of rude behavior, dressing in a deliberately provocative/shocking fashion, rounds of public tonsil hockey with skanky-looking young men... sensible parents, regardless of denomination, don't wait till AFTER the drug abuse or first pregnancy to start worrying.
And again, those things are not enough, in themselves, to convince a mainstream audience that a teen character is genuinely troubled. They're too common, and generally outgrown without incident. Thus this trope. Whether a parent considers such behavior unacceptable or not is up to them.