I think the biggest difference is the fact that Filomenas boss (ahemmm a lawyer) came to the scene of the crime shortly after Filomena called him. Very shortly after the discovery of the body.
She also made Knox call police when she knew perfectly well Knoxs Italian was limited at best. And rather than call Merediths phones herself she asked Knox to do that. Why?
Nothing in evidence makes Knox a better candidate as a suspect than Filomena...nothing except for the smoke and mirrors.
Personally I think that the time line after the murder is far more interesting to me. Watching as the whole thing evolves and noting when the police formed their conclusion and started with confirmation bias.
It was actually pretty early on.
The police jumped to the conclusion that the burglary was staged, and from here they started to go wrong. There were a number of reasons for believing that the scene was staged, but a lot of them just don't stack up when actually viewed in the light of day.
* It would be hard to throw a rock through the small gap in the outer shutters. (Mignini)
This assumes that the position of the shutters when the rock was thrown was the same as the position of the shutters the next morning. However, an intruder could have easily opened the shutters from the outside (Filomena notes that she was not able to pull them tight and lock them due to the wood having expanded) then thrown the rock through the now entirely open shutters, before closing them once more after entry. Of course since they were hard to close, any intruder would likely pull them shut but not enough to prevent the wind popping them open leaving them half open as they were found in the morning.
* Nothing appeared to be taken (Various people)
While laptops were obviously not touched (with perhaps the exception of Filomena's which had fallen over) crime scene photos indicate that someone had gone through several of the girl's drawers. It may well be that an intruder was after money or pot and considered the laptops hard to dispose of. Since we know that any intruder would be Rudy and that he had previously stolen a laptop which he had had difficulty getting rid of, and was eventually caught with, the odds are that he would not be willing to try taking and fencing those items again. The girls were unlikely to have told the police if their dope was missing.
* No glass outside (Various people)
The larger shards of glass will be propelled into the room with the rock. Tiny slivers will go outwards, but these will not be easy to see, and there was no serious forensics done in this area to look for such small shards, in fact the police trampled all over it and used it as a smoko area thus destroying any evidence that would have been there.
* Wrong window to choose (Mignini)
The claim is that no burglar would have chosen this window to gain entry. This is because it is visible from the street, driveway, and car park area. Suggestions have been made that the better place would have been the balcony/patio on the other side of the house. In fact this is incorrect. Filomena's window is poorly visible from the road until you are almost opposite the cottage, the street lights are behind a row of trees above the driveway meaning that it is shaded. While visible from the drive and car park area, it also allows any intruder the ability to throw a rock from the car park area and should that disturb anyone inside, retreat up the drive with relative ease. It also allows an intruder the ability to drop down into the darkness of the lower lawn should they fear being observed. These are all positives for picking this window for entry. The balcony is visible from a large part of the road to the east of the Cottage meaning that anyone travelling from that direction would have a clear view of it. There are streetlights right across the road that would light the balcony and once on the balcony there is little chance of making a quick and easy escape if the intruder fears being spotted or disturbs the inhabitants of the cottage. These are serious disadvantages for picking this way of entry.
Once this fateful decision has been made (that the burglary was staged) the case takes the wrong turn.
With the police now sure that it was staged, they make the assumption that a staged burglary means the killer(s) tried to throw the scent off onto a stranger, which must mean that the killers were known to Meredith. Without a way to enter the Cottage (with the window ruled out) the only entrance is via the front door, and that requires a key. That means that the killer was one of the housemates. Laura had an iron cast alibi so this left just Knox and Filomena. Filomena lawyered up, and according to many people, Knox's behaviour was strange, so the police turned their attention to her.
At this point I suspect that the police didn't consider her as a killer, but rather involved. The initial reports put black hair in Meredith's hand, and I suspect they were after a black suspect based on this and the CCTV footage of Rudy. Knox again fit the profile they were building because she knew and had a close relationship with a black man, her boss Patrick, someone else that knew Meredith. Gaining her phone records would have shown them the texts from and to Patrick on the night in question, further adding to the fire and then there is the meeting between Knox and Patrick where Patrick questioned how the case was going.
I firmly believe that police were following Knox by this stage and so would have certainly noticed and reported this meeting. I believe that this is the point that the police decided that they had solved it. Knox had meet with Patrick as suggested by the texts between them, they had gone to the Cottage where Patrick having a crush on Meredith had attempted to get her to have sex, and failing, he had killed her. It all made sense at this point, except that Knox still had an alibi, Raffelle.
So they called them in. The objective of that night was to first break Raffelle's alibi for Knox and then once they had done that, use what they had, and a few lies to get Knox to crack and give up their prime suspect, Patrick.
Once they had convinced Raff that it was possible that Knox had left, they called in Knox and confronted her with the evidence. Raff dropping her alibi, saying she left. The CCTV footage of her going to the cottage (Which they believed was Knox at the start but was likely Meredith.) The texts between her and Patrick saying they would meet up. Telling her that she was lying each time she denied it, telling her that they knew the truth and that unless she told them what had happened she was going to jail for 30 years.
When that failed, they brought in the "interpreter" to do the whole local amnesia trick, convincing her that the evidence proves that she was there, they had her on tape going there, they had proof that she was in the cottage with Patrick, so the only reason she couldn't remember was that she was traumatised, that if she really wanted to help, she should try and remember, try and imagine what had happened to Meredith that night. This time it worked, the techniques used created a false memory as she "imagined" what happened.
And at that point it all fell into place for the police. They knew what had happened, and Knox confirmed every part for them. The fact that she only told them what they had already told her didn't matter, they had her "confession" on paper. Case Closed.
The issue of course it that everything the police thought was true in those first few days would turn out to be completely wrong, and so likewise, because it was feed to her by the police based on what they thought they knew, everything in Knox's "Confession" is also totally wrong as well. The irony of this seems to have been missed by a lot of people.