Crown prosecutor Philip Morgan, QC, spent some hours traversing the DNA found on Mark Lundy's polo shirt, which police discovered in his car when he returned from a work trip to Wellington.
"Put it all together and Mark Lundy has Christine Lundy's brain on his shirt," he said.
But Mr Hislop suggested it was not that simple.
"Of course there were two horrible horrible deaths, of course there was brain everywhere. The fact brain was found on his shirt is not the end of the story," he said.
Mr Hislop said the issues of potential contamination were "deeply concerning" and singled out Detective Senior Sergeant Nigel Hughes, who was responsible for the crime scene.
"The book stops with officer Hughes. If we're concerned about the level of professionalism, we have to be concerned with anything found in that crime scene," he said.
He was not the only witness who came under fire.
Mr Hislop also took aim at police computer expert Maarten Kleintjes who at the first trial gave evidence the Lundy family computer clock may have been manipulated.
When the Crown's new theory of Lundy travelling home in the early hours of August 30 rather than several hours earlier no longer fitted with that evidence, he said the witness changed his story.
"The time of death hypothesis changes... what do you know? Kleintjes is telling a different tale because he has to," he said.
The partly-digested stomach contents of the victim was a plank of the Crown case in the first trial but the defence said it now served to debunk the new version of events.
Mr Hislop said Amber would have had to get up after going to bed to eat warmed-up McDonalds for her stomach to contain food when the Crown alleged Lundy committed the murders.
"Absolutely preposterous," the lawyer concluded.
He continuously told the jury the Crown had "tunnel vision" and forced the evidence to fit its case rather than keep an open mind.
But Mr Morgan was confident there was only one logical conclusion the jury could reach.
"Viewed collectively, [the evidence] demonstrates beyond any question of doubt it was the accused who killed his wife and his daughter," he said.
"The car tells us how far he travelled, the shirt tells us where he went and who he did this to, the paint flakes tell us what he did it with, the scene tells us what he did, witness X tells us why Amber had to go too and the finances tell us why."
The defence closing is expected to conclude tomorrow.