In its final acquittal order, the NIA court pointed out several critical lapses by the prosecution and investigating agencies in the 2008 Malegaon blast case. The prosecution failed to establish that the explosion occurred inside a scooter allegedly owned by BJP MP Pragya Singh Thakur. Key forensic procedures were also ignored — DNA samples were never collected from the blast site, and the area wasn’t barricaded until one hour and forty five minutes after the incident.

The Anti-Terrorism Squad (ATS) was accused of torturing and coercing accused individuals into giving false confessions. The court noted that several witnesses were forced to give statements under duress, with allegations of physical assault and intimidation by investigators.

The court submitted approximately 1500 pages detailing the reasons for acquitting all seven accused. A total of 323 witnesses were examined during the trial. After the case was transferred from the ATS to the NIA, it became apparent that the accused may have been forced to confess to crimes they did not commit.