Michael Reed QC accused Mr Hentschel of inadequate record-keeping in his work during the investigation into the 1994 murders of Bain's parents and siblings, particularly in the taking of blood samples from the Winchester .22 rifle used in the killings.
Mr Reed said scientists in the United Kingdom were "shocked" at Mr Hentschel's poor recording of his examination of items at the murder scene and of his failure to ensure items from the house were retained for further testing at a later date.
The fact areas of carpet where luminol testing had revealed bloody sock prints had not been cut and kept meant it was not possible for other forensic scientists to do further testing of the prints, Mr Reed said.
The size of the prints and whether they would have been made by a foot larger or smaller than the prints themselves was the subject of extended defence questioning on Wednesday.
The Crown says the prints were left by the killer and the defence says that because the carpet was burned with the house two weeks after the shootings, they have been unable to have more tests done which, they say, could have exonerated David Bain.
Asked whether he gave evidence spectacle frames found in David Bain's bedroom were damaged on the right side because that would coincide with an injury on the right side of David Bain's forehead, Mr Hentschel said he believed the damage was to the right side of the frames.
When told by Mr Reed that an ophthalmologist had described the damage being on the left, Mr Hentschel agreed it was another area "where opinions could differ".
He also agreed he had made no notes or diagrams of exactly where he took a sample of blood from the forearm of the rifle near four fingerprints.
He said it was near the fingerprints, about 5mm to 10mm from the last print.
He had taken the sample in the presence of a fingerprint expert who was shining a polylight on the area and the sample was taken "as close as possible to the area of the prints".
Mr Hentschel denied he had mislabelled the blood sample as being "from the fingerprints".
As far as he recalled, he had not told the first jury the sample was from the fingerprints, but from the area where the fingerprints were.
If the Crown had told the jury at the first trial the blood was from "under the prints", "then they've misinterpreted what I said".
Mr Reed asked Mr Hentschel to explain why scientists examining the rifle in 1997 found blood smearing between fingerprints on the forearm, when the witness himself said he had seen no smearing in 1994.
Mr Hentschel said he could not explain it because the examination by the other scientists was carried out "some time" after he had seen the rifle which had gone through several hands and a number of tests in the intervening years.
Pressed further, he said it could have happened through people handling the gun or touching the area - "I don't know".
Asked if he was suggesting there had been "pretty incompetent handling by the ESR" and that they had placed blood on the gun, the witness said he was not suggesting that.
He was then asked why the two other scientists found only two fingerprints on the rifle in 1997, not the four Mr Hentschel said he was shown in 1994.
"I don't know why they found only two prints," the witness said. "I certainly did not remove them."
Mr Reed said Mr Hentschel's examination was inadequate from a recording point of view and that he had provided insufficient information for other scientists to reinterpret.
"I believe I've done sufficient," Mr Hentschel replied.
Re-examined by Crown counsel Kieran Raftery, the witness said no other scientists had approached him to ask for help in reinterpreting his notes "nor have any defence counsel".
He said he believed the note-taking he did in 1994 was of the standard used at that time.
And, on the question of the bloody sock-print, his opinion was still that the foot which made the print was larger than the 280mm print.
