Investigators across the globe are trained to recognize a staged burglary. Glass on top of the ransacked items, absence of evidence beneath the broken window, and deductive reasoning meant that of all occupants of the upstairs flat at the cottage, Knox could be the only culprit. That is, given that the scene was staged, someone with a key had to be involved, and both Laura and Filomina had clear, verifiable explanations of their activities on the night of the murder.
Additionally, Knox made the unusual statement that Meredith routinely locked her bedroom door, which appears to be an attempt to delay the discovery of the body. Knox and Sollecito lied repeatedly to police about their activities on the night of the murder. Those lies had to be investigated, identified as lies, and then the culprits had to be re-interviewed. However, that did not result in tunnel vision such that police only investigated Knox. In fact, many people were interviewed over several days. Knox remained a witness, just like the other parties that were interviewed, until she made a statement placing herself at the scene of the crime at the time of the murder.
In terms of evidence, there was a bloody footprint on the bathmat, bloody footprints in the hallway, prints in the bedroom, blood in the small bathroom and so on. Why should police look only at a palm print or a shoe print when there was also a bloody barefoot print? Why not look for the person that created the bloody footprint, or the person that could be responsible for staging the burglary?
Yes, why not match all the prints available? Why not take more prints from other areas of the cottage and prints from more people that were known to have been in the cottage?