Police, Botha acknowledged, left a 9mm slug from the barrage that killed Reeva Steenkamp inside a toilet and lost track of illegal ammunition found inside the house. And the detective walked through the crime scene without wearing protective shoe covers, potentially contaminating the area.
Pistorius says he mistook Steenkamp for an intruder and shot her out of fear. Prosecutors say he planned the killing and attacked her as she cowered behind a bathroom door.
The day seemed to start out well for the prosecution, with Botha offering new details of the shooting that appeared to call into question Pistorius' account of the moments leading up to the 29-year-old model's death.
Ballistic evidence, he said, showed the bullets that killed her had been fired from a height, supporting the prosecution's assertion that Pistorius was wearing prosthetic legs when he took aim. The athlete has maintained he was standing only on his stumps, and felt vulnerable and frightened as he opened fire from a low position.
But, when asked if Steenkamp's body showed "any pattern of defensive wounds" or bruising from an assault, Botha said no. He again responded no when asked if investigators found anything inconsistent with Pistorius' version of events, though he later said nothing contradicted the police version either.
Testimony began with the prosecutor telling the court that before the shooting, a neighbor heard "nonstop" shouting between 2 and 3 a.m. at Pistorius' upscale home in a gated community in the capital, Pretoria.
However, Botha later said under cross-examination that the witness was in a house 600 yards away, possibly out of earshot. He cut that estimate in half when questioned again by the prosecutor.
At one point, Botha told the court that police found syringes and two boxes of testosterone in the bedroom - testimony the prosecution later withdrew, saying it was too early to identify the substance, which was still being tested.
Still, Botha offered potentially damaging details about Pistorius' past, saying the athlete was once involved in an accidental shooting at a restaurant and asked someone else "to take the wrap."
The detective said police found two iPhones in Pistorius' bathroom and two BlackBerrys in his bedroom, and none had been used to phone for help. Guards at the gated community did call the athlete, Botha said, and all he said was: "I'm all right," as he wept uncontrollably.
Roux later suggested that a fifth phone, not collected by the police, was used by Pistorius to call for help.
The question now is whether the troubled testimony will be enough to convince Chief Magistrate Desmond Nair to keep Pistorius in prison until trial. Final arguments were scheduled for Thursday.