So York goes into Thomas' apartment to look for clues. After York finishes profiling, a bottle behind him shatters for no apparent reason. York takes this as a sign that Thomas wants him to look around more? I assumed Thomas was trapped in crazy land and he was poltergeisting the bottle to break and reach out to York. But it turns out Thomas is one of the bad guys. 
 
Or it might just be an homage to Twin Peaks without any real connection to the game or reason for it happening.
 
For those of you not in the know, Dale Cooper uses a Tibetan investigative technique wherein he throws rocks at a bottle each time a name is read off a list of possible suspects. Missing the bottle means he's cold, hitting the bottle without shattering it means he's warm, and shattering the bottle means he's on the money.

I assumed it was the sound of Thomas trying to leave the appartement.
 George and Emily run in after that and the camera zooms in to the window. Then they say dammit and leave to chase after him.

I thought they wanted to give chase because they just entered the apartment and saw it was empty and the camera pan was towards the broken bottle.  
 
It's hard to tell what this game is trying to tell me sometimes.

I don't think it was ever established that when you are in the crazy world you are parallel with the real world, in the same sense of how the Silent Hill movie worked.

Wasn't it a lamp that shattered?

I try not to think about it too much.

Yeah, that didn't make sense to me either when they came across it in the ER.  My guess is you're probably right and it is just a Twin Peaks reference that is not meant to have a rational explanation within the universe of DP.

Thomas wasn't really one of the bad guys.  I mean...  not really.  I'm pretty sure George intentionally led York to the empty apartment to make sure that York saw the red wig (which he planted hairs from at the lumber mill- remember, it was stuck in the gears of the elevator) and the women's clothing (since he'd made sure to mention that he was sure the killer was also the one wearing the heels in the initial forensics cutscene at Anna's crime scene, though York disagreed.)  Sure, Thomas snaps, but that's only after finding out his boyfriend was framing him for crimes he'd committed, which kind of sucks.  (I believe George may have made Thomas transcribe the Red Seed legend, and this may have been when he realized it.)
 
I think by the time York gets to the apartment, Thomas is already gone, possibly in the bar dungeon.  I think the bottle smashing was a sign that there was more to uncover- York seems to say as much- and I believe the later dialogue implies that the "bonus footage" that York is looking for is in fact "still part of the main feature" and that the object it was referring to is George's tree-patterned locket from Kaysen.