Defense lawyers also complained that the police did not make results of some biological tests available to them.
The complaint was made by laywyers for Knox's ex-boyfriend and co-defendant Raffaele Sollecito.
"We have been working with our hands tied behind our backs without access to essential evidence that would have allowed us to do pre-emptive analysis and might have led us to different conclusions. I don't even know if Raffaele would be in prison," Sollecito's lawyer Giulia Bongiorno said.
Knox, 22, of Seattle, and Italian native Sollecito, 25, have been on trial in Perugia, Italy, since January, accused of sexually assaulting and murdering Meredith Kercher, a 21-year-old British exchange student who shared a scenic cottage with a view of the Umbria hills with Knox. Kercher was found seminaked with her throat slit on Nov. 2, 2007.
Sollecito's defense team raised the issue during the testimony of Professor Adriano Tagliabracci, a legal doctor and consultant for the team.
Tagliabracci contested traces of Sollecito's DNA found by the forensic police on Kercher's bra clasp. The clasp wasn't found until a second searach of the apartment more than a month after the murder.
The doctor argued that the evidence was ''not properly bagged and missed for 47 days, when it was found in another location during a search of the bedroom on Dec. 18," he said.
''The clasp goes from one scientist to another, and we don't see gloves being changed. We then see it being put on the floor and picked up again. These procedures are all wrong," Tagliabracci testified.
''By not changing gloves and by touching other objects, cross-contamination of DNA is highly possible,'' he said.
Under the complicated Italian legal system, the court has only been sitting twice a week as Judge Giancarlo Massei and the prosecutors and defense teams are involved in other trials.
After today's hearing, Knox's mother, Edda Mellas, said she will go back to the U.S. and return to Italy for the beginning of the hearings in September.
"It's a long process, you know there were weeks when there were no hearings, sometimes there was one or two," Mellas said, complaining about the slow pace of the trial. "The prosecution was allowed to take a very long time to slowly present their case. […] So now there'll be a two-month break where everybody goes on vacation except for us. We'll be sitting here waiting for two months and then we'll start up again."
However, she said her daughter is staying patient and keeping positive.
Prosecutors believe Knox, Sollecito and a third person, Ivory Coast drifter Rudy Guede, 22, killed the British woman in what began as a sex game.
Both Knox and Sollecito deny wrongdoing. Sollecito has said he was at his own apartment the entire night of the murder. Knox said she spent the night at Sollecito's apartment and went back to her place the following morning. Sollecito said he did not remember if Knox spent the whole night with him or just part of it.
Guede was found guilty of murdering and sexually assaulting Kercher; he was sentenced to 30 years in prison last October.
A verdict is not expected until early November, the second anniversary of Meredith Kercher's death. If convicted of murder, Knox and Sollecito could face Italy's stiffest punishment, life imprisonment
Enzo Beretta from Perugia contributed to this report.