Why didn't Virginia call the police after she trapped the trolls in the elevator or after Wolf attempted to eat her grandmother?
Because both of those situations were way too crazy for the police to believe?
Not really, they're basically just a flamboyant serial killer and a weird looking street gang as far as she knows at that point.
She knows the dog can understand human speech, so she's probably taken the trolls at their word that they are trolls. If she called the police about them, or Wolf, she'd be asked a lot of questions and probably start babbling about intelligent dogs and look crazy. She's spooked, she's not in the clearest frame of mind.
Why does Prince Wendell's voice sound muffled when he's holding a pencil in his mouth? He speaks via telepathy, if that.
It's not telepathy, it's magical translation of Dog to English.
Why is it the key Tony got the Tooth Fairy to make didn't work on the door? I can see three explanations:
It was the wrong key.
The watch Tony gave the Tooth Fairy was in fact fake (lampshaded by him having doubted its authenticity himself as a Call Forward to this moment), so the Tooth Fairy retaliated by making a faulty key.
There was a prong or other shape to push aside tumblers on the other side of the key which didn't get reproduced, since the impression in the soap was only for one side. (See Indiana Jones and Toht only having one side of the medallion burned in his palm.)
What happened when Wolf gave his will to the Queen? She gave him a very intense stare and it appeared to be magically binding, but afterwards he seemed to have the power to disobey her when he wanted to. Was it magic, or just a regular promise to serve her?
Was there some kind of romance between the Huntsman and the Queen? In his first scene, he kisses her hand and she presses it to her cheek, but its never hinted at again.