Old Bailey jurors had been told how a bloodstain on the same trainer went undiscovered for four years after forensic scientists missed it.
The shoe is said to belong to the younger brother, aged 12 at the time of Damilola's murder.
Prosecutors allege he was one of three youths involved in a failed robbery of 10-year-old Dami in Blakes Road, Peckham, on November 27, 2000.
The little boy was stabbed in the leg with a broken beer bottle and bled to death after staggering up a litter-strewn stairway on the North Peckham Estate.
Jurors watched a video made by detectives five days after Dami's death at the younger brother's room in Cator Street, Peckham, showing a row of trainers and other clothing said to be important to the case.
But Orlando Pownall QC, defending the boy, who is now 17, suggested the officer had made mistakes cataloguing "the all-important pair of trainers".
He told the hushed courtroom officers had wrongly claimed the shoes were discovered in a bin liner when the video revealed they were found on the floor at the end of the bed.
In another alleged blunder, Mr Pownall claimed officers had risked contaminating evidence by failing to wear protective suits when they arrested the same 12-year-old boy and seized his clothing.
Detective Constable Paul Davis told jurors he and his colleagues did not separately seal the items, including a puffa jacket, sweatshirt and jeans, before taking them away. He told the court they had arrived at a children's home in the early morning of December 2, 2000.
DC Davis said he and DC Michael Coshall had not worn protective clothing when they collected exhibits from the bedroom to cause "the minimum amount of disruption".
Four youths were charged with Damilola's murder but acquitted at the Old Bailey in 2002.
But new blood and fibre evidence found when cops ordered a second examination of the items allegedly links three youths to the killing who were questioned at the time but never charged.
Hassan Jihad, 20, of Consort Road, Peckham, and two brothers from South London aged 17 and 18 who cannot be named, deny murder, manslaughter and assault with intent to rob.