The "corrupt cops" allegation:
There were indeed corrupt cops, and Joey Allegretto (James Gandolfini) was one of them, and was out to kill drug boss Jordan Washington (Shiek Mahmud-Bey) because he wouldn't increase the bribes. Joey also lied in court about not knowing bribe distributor Kleinhoff. However Joey's partner Liam Casey (Ian Holm) was not corrupt. Joey commits suicide.
The missing arrest warrant:
The original arrest warrant had run out the day before, and cop Liam Casey had written a new one and forged the signature, hoping to make the biggest arrest of his career. He tells this to his son Sean Casey (Andy Garcia), who became the new District attorney thanks to his performance in the court case against the drug boss. His girlfriend (and assistant to the Dershovitz-like attorney who represented the drug boss) Lena Olin (Peggy Lindstrom) finds the original arrest warrant and takes it, but gives it back to Sean Casey, who shreds it. At the same time, cop Liam Casey turns himself in to Judge Impelliteri (Dominic Chianese), who had signed the original arrest warrant. The Judge calls Sean Casey and tells him that he "absolutely remembers signing an arrest warrant on that date", asks the cop for the date, and signs a new arrest warrant, and tell the DA to shred the old arrest warrant.
The film ends with DA Casey explaining to a new crew that the world isn't black and white.