The High Court in Johannesburg sitting in Palm Ridge heard that a bullet recovered from the three-year-old's head and another bullet found inside Keenan Mokwena's car had come from similar guns.
Mangena said the bullets had similar class characteristics -- meaning they came from similar firearms -- but there were no individual characteristics to prove that both bullets were fired from the same gun. This was due to the type of bullets that had been used.
Khakhu, 22, is on trial for the murders of Tibbetts in August 2014 and Alton Mooi in June 2013. He also faces five counts of attempted murder, 10 counts of the unlawful possession of a firearm and ammunition, and one count of pointing a firearm.
He has pleaded not guilty to all charges.
On August 2 last year Khakhu allegedly shot at a white car Mokwena was travelling in along Steytler Street in Westbury, Johannesburg.
Mokwena was driving away from Khakhu after pointing an alleged toy gun at Khakhu to scare him.
Tibbetts was in a car with his family travelling in Khakhu's direction as he was shooting at Mokwena's car while it drove off.
A stray bullet hit the car's windscreen and struck Tibbetts in the head. He died six days later in hospital.
The court heard on Wednesday that Tibbetts had been sitting in the centre of the back seat of the vehicle, on his mother's lap.
Mangena told the court no firearms were retrieved during investigations, which made evidence gathering difficult.
"There was a murder case without a crime scene but we heard that there was a shooting, and that vehicles were involved," he told the court.
To re-create what happened on the night of the shooting Mangena had to use the bullet cartridges and fragments found on the street as well as the cars that had been involved.
Mangena found that no bullets had hit the silver car Khakhu was standing near on the night of the shooting. There were also no bullet holes found on the walls on the side where the silver car had parked.
Witness Dalmain Abrahams testified on Tuesday that Khakhu was the only person he saw firing shots.
Mangena said bullet holes were found in Mokwena's white car but only three had penetrated the car.
Judging by the direction the bullets were travelling in, the shooter must have been standing in the middle of the street, Mangena said.
The bullet which hit Tibbetts in the head "was a straight hit from the firearm to the windscreen," he told the court.
He disputed the fact that a bullet that fast and direct could have come from the left back seat of the white car, where Mokwena had been sitting.
"Based on the trajectory of the bullets into the white Yaris, the shooter must have been standing in the middle of the road," Mangena said.
No evidence of shots fired towards the area of Khakhu and the silver vehicle, was found at the scene.
Sog Van Eck, for Khakhu, suggested to the court on Tuesday that Mokwena had lied by claiming he pointed a toy gun at Khakhu, because that point was not part of his statement to police.
Mokwena insisted it was a toy gun.