I realize I'm a bit of a latecomer to this thread, but there was a "thing" in season two that got me, and now in season three, there's another thing that has me downright irritated.
Season 2: Daenerys is one of my favorite characters. Yes, she's not the greatest by any stretch, but there's something about her. In the books, I'm always pleased to come across her chapters (until DwD where she seems to stall out for some reason). Now, I know that there are always changes made between books and film/tv. (I'm an amateur filmmaker myself.) So my issue is that throughout the whole of season two, Dany is just so passive. In the books, she's taking baby steps toward finding herself and becoming a responsible ruler, but she's actively taking those steps. (Obviously she seriously comes into her own in SoS/season 3.) But it seems like throughout most of season 2, she's just along for the ride. She's whisked here and there, passive with Xaro, and the whole "Where are my dragons!?" times a million seemed kind of ridiculous. In CoK, she willfully goes into HOTU to seek knowledge, not because something precious was taken from her, forcing her to action. That makes it reaction.
At the end of the day, it's a minor thing, and they've adjusted/corrected in season 3, but it was something that kind of annoyed me.
Season 3: What the hell are they doing with Sam? He wasn't a total loser that they've make him out to be, with Mormont's comment, "Did you get the ravens off?" and Sam shamefully shakes his head. In point of fact, yes, he did get the ravens off, almost all of them. He sort of failed to attach messages to most of them, but he did get them off. So he's not as inept as they made him out to be.
And Sam the Slayer! Sam who slew an Other! All the black brothers are impressed as hell, giving him praise and laud (which funnily makes Sam embarrassed, being heralded as some sort of hero, the antithesis of his own self-image). He's badass! Why they would take that away from him is beyond me, and it really bothers me. I like Sam, and this whole situation is what really makes him start coming into his own. As for the series...
"Dear Sam: You just slew an Other with your dragonglass dagger. You're the smartest one of the brothers, bar none (okay, maybe Aemon), so after you do some quality slaying and grab the girl to flee, get the damn dagger! Seriously bro? Really? Sincerely, Lily."
And on that note, Sam's the one who, while still with all his brothers, is all "Dragonglass! Dragonglass is the answer! Arm yourselves with all the dragonglass we have!"
Just my two cents.