Alright, since you asked! :) I admit that I notice these things mostly because of my personal issues and I am in NO way trying to say that because I see something wrong with the show you should stop watching it or anything but

I really don't like how they handle the subject of mental illness. They basically add to the telly stereotype that if you're mentally ill then you're dangerous. They actually name psychiatric diagnoses when the plot doesn't require it. Even Will, whose job is understanding these people, doesn't display an ounce of sympathy for them and it's written like "poor Will, he has to get in the heads of those bad gross people, ew". And that thing with season 2 poster of restrained Will with a caption "Embrace the madness' is just appalling, hell, it's 2014 and human rights and psychiatry made at least some step forward since Silence of the Lambs was written.

I'd let it go but it's kinda ironic all this goes on while people on tumblr rant about how Steven Moffat "set feminism 50 years back" just because a female character fell in love with a male character or something.

That and sometimes it's just illogical. That guy with a brain tumour - how did he kill himself again? How is that physically possible?

I could go on but I realise that the rest of it is probably repetitive and stems from me being upset about the issue I described above, so I'm sorta used to looking for flaws at this point. :)