In the 1,036-page judgment of the Malegaon blast case, the special NIA court judge, A.K. Lahoti, has expressed serious concerns regarding the methods of torture and illegal detention allegedly employed by officers of the Maharashtra Anti-Terrorism Squad (ATS). The judge found merit in the allegations that the ATS had not only tortured witnesses but also planted evidence. These observations echo similar concerns raised by the Bombay High Court in the 11/7 train blasts case judgment, where the court discarded evidence that led to the imprisonment of 12 men for nearly two decades.

While the special court dismissed torture claims from acquitted accused Pragya Thakur and Lt Col Prasad Purohit, it found credible the claims of accused Sameer Kulkarni regarding illegal detention. The court's findings have prompted questions about the credibility of the evidence collected by the ATS during its investigation. The special court has directed that a copy of its judgment be sent to the Director General of ATS and the NIA for review and necessary action.

Several witnesses in the Malegaon blast case, 39 out of 323 who later retracted their statements, alleged torture by the ATS. One witness claimed ATS officers forcibly took him to Nashik, interrogated him late into the night, and threatened him to make a statement aligning with their narrative. Feeling pressured, he gave a statement as dictated by the ATS, which he later claimed was baseless, and filed a complaint against the ATS officers with the Human Rights Commission. The judge noted the possibility that the witness's statement was obtained through coercion and threats.

The Bombay High Court, in its July 21 judgment concerning the 11/7 train blasts case, also expressed serious doubts about the integrity of the ATS's investigation methods, holding that confessions were a result of custodial torture. The court detailed brutal methods allegedly used by the police to extract confessions, including forcing individuals to split their legs 180 degrees, tying them to chairs overnight, denying them food for extended periods, placing cockroaches in vests and rats in underwear, and severe beatings. The High Court stated that such methods, while leaving no visible scars, could severely bruise the mind and injure the psyche.

Special Judge A.K. Lahoti noted that almost all witnesses testified that they had not given their statements voluntarily but under coercion by ATS officers. The judgment highlights that allegations of misconduct, torture, and illegal detention were exclusively against ATS officers and not against officers of the National Investigation Agency (NIA), which later took over the case. This disparity raised serious concerns about the credibility of the evidence gathered by the ATS.

The court also addressed the prosecution's failure to examine key material witnesses, noting that the statements of the witnesses presented did not sufficiently support the prosecution's case. While acknowledging the prosecution's discretion in selecting witnesses, the judge stated that if relevant witnesses are not examined, the court may draw an adverse inference against the prosecution.

Furthermore, the special court, in its judgment, rejected claims made by a former ATS officer, Mehboob Mujawar, that he had been ordered to arrest RSS chief Mohan Bhagwat in connection to the case. Special NIA Judge A.K. Lahoti stated that he did not find any merit in the contentions made by the advocate for accused Sudhakar Dwivedi, who relied on Mujawar's claims.

In acquitting the seven accused, the special court also debunked the prosecution's claim that right-wing extremist group Abhinav Bharat was involved in the blast, noting that the government had not banned the organization as a terror outfit. The court observed that the prosecution failed to prove that the Abhinav Bharat Trust was formed to establish a Hindu Rashtra or to change the Constitution of India and that funds collected by Abhinav Bharat were used for illegal activities.

The special NIA court also pointed out that neither the Maharashtra ATS nor the NIA was able to establish how RDX was sourced, transported, or assembled for the explosion. The court dismissed conflicting theories presented by both agencies as unsupported by credible evidence.