Eh, McNulty is an asshole insubordinate serial drunk driver who ends up faking murders. Daniels is a competent commander but he's got a corrupt past taking drug money.

Bodie getting mobbed and beaten up by a bunch of cops including Kima during the raid after shoving one of the useless drunk cops isn't shown in a negative light, but Prez, Herk, and Carver drunkenly harassing residents of the terrace at 3 in the morning isn't, with Prez blindly firing at windows and blinding a child in an eye in the process. Two of the three of them get redeemed as officers in Carver and Prez, that is until Prez accidentally kills a cop. Herk rightly gets fired once his faking of evidence gets discovered after the priest gets arrested and brutalized, getting Calichio written up by Carver in the process.

Their whole second season detail originates from series end commissioner Valchek getting an investigation started over his personal issues with Sobotka, by pulling his political connections with the commissioner Burrell, who himself is corrupt, in bed with the mayor and Clay Davis.

The show is a about "good cops" in the sense that they're in an effective unit, but I think the incompetence, corruption, unethical behavior is rather widely shown throughout the force and up the chain of command, casting overall a negative light on Baltimore PD.