A couple spoilers below, yada yada, don't be in the damn spoiler section and then bitch at me that you read some.
1) Their unlimited ammo is really starting to bug me. This came to a head when you gave Clementine the colt you took from Chuck's body, that he (Lee) SAYS is out of ammo if you try to use it on the grate at one point, but apparently since then he managed to find a bunch of shots for a revolver? Not to mention the fact that it is, in fact, a REVOLVER. The girl's 8 years old - The recoil on a gun that size could EASILY dislocate her shoulder. But the ammo thing is more important - It's really hard to take 'Oh we're so hungry' seriously when at the same time they go 'GOOD THING WE FOUND AN UNLIMITED SUPPLY OF PISTOL/SHOTGUN/RIFLE/REVOLVER AMMO EARLIER AND OFF SCREEN'. ((This one was answered. Apparently it was Vernon's revolver. I totally forgot about it. Still doesn't explain her lack of injury though))
2) How did the zombie Clem kills if you leave her behind get in ANYway? You saw that place - it was barricaded to hell! And when they come in, it's not like any boards are missing. So what the hell? Did it just teleport in?
3) The barricades in that house themselves. They spend that huge time OMG HOW DO WE GET IN, THE ONLY WAY IS THIS DEAD DOG... Then the FIRST thing you can see upon entering? A window in the kitchen, along the same wall as the backdoor, that's wider than the doggy door and complete free of any barricades. Nice.
4) As another example of wasting so much time. They spend forever trying to bust into the armory of the Catholic school. Then what's the first thing they find? "Oh look, this door just opens to the hallway, and doesn't even seem to be locked". Yeah I'm sure Crawford DEFINITELY would've allowed that kind of liability. ((So, I'm being told this was a downstairs hall. Still seems weird Crawford would allow that loophole though))
5) Seriously, how the hell did Lee get back from visiting the motor pool the second time? The first time they had to go all parkour and leave through the roof. The second time, when he leaves, he sees a zombie blocking the _only way out_, since going through that way is the only option now - every other way is a) The motor pool filled with zombies (leading to a jump we KNOW he can't make without Molly) or b) A barbed wire fence.
6) Vernon. I got listed as being honest with him, and I only threatened him to get him to drop the gun - after that I apologised and was asking nicely to get him to come with me. And yet he still went YOU'RE A DICK LOOK HOW YOU MADE ME COME. I'm just sitting there like "...You mean asking you?"
Any I missed?
Edit: Fixed some typos and the part where I accidentally called the school a church.