The plea was made by Jamiat-Ulema-e-Maharashtra, an NGO, which is providing the accused free legal aid.
In the application before a designated Maharashtra Control of Organised Crime Act (MCOCA) court, the accused said there were contradictions in the earlier charge sheets filed by Maharashtra Anti-Terrorist Squad, Central Bureau of Investigation and National Investigation Agency (NIA).
The accused alleged that they were falsely implicated in the case and urged the court to direct the Commissioner of Police or any other competent authority to initiate a departmental inquiry against erring police and ATS officials.
The NIA had concluded that their confession was not voluntary and had been allegedly obtained from the accused under duress, said lawyer Sharif Shaikh, who provides free legal aid to the accused through Jamiat-Ulama-e Maharashtra.
The court had earlier granted bail to seven accused facing charges in the Malegaon blasts after NIA probed the case and submitted its primary report in November 2011.
Four bombs had exploded in Malegaon on September 8, 2006, killing 37 people, on the occasion of 'Shab-e-Baraat', considered auspicious among Muslims, when they assemble to pay respects to their departed kin.