As far as I can tell, Port of Call is the first produced feature script by a TV writer, although on imdb they've credited all four writers of the original as well, perhaps because there are so many plot / thematic similarities between the two movies.
Both "bad lieutenants" (i) take drugs; (ii) gamble; (iii) abuse their authority to obtain drugs; (iv) abuse their authority to obtain sexual favors; but also (v) do actually care about their role as homicide investigators and pursue it vigorously.
Additionally, the arc of both movies is similar, with a traumatic event haunting the lieutenant (original: massive gambling debt accruing as the Mets come from behind to beat the Dodgers in a seven game series; Port of Call: constant pain due to an injury suffered during Hurricane Katrina) as he relentlessly investigates a horrendous case (original: Nun raped in a church by young hoodlums; Port of Call: immigrant family slaughtered by drug lords).
Both films bear the distinctive stylistic marks of their respective directors.
But one can see the origins of Ferrara's hatred of the Herzog not-really-a-sequel, perhaps, in the radically different messages of the two films.
Ferrara's is a complex Catholic passion play. In his quest to solve the rape / desecration case, the lieutenant (re)discovers the significance of sacrifice and forgiveness in the attitude of the nun, who refuses to identifier her assailants because she has already forgiven them. Ultimately, promising her the justice she wants, he discovers their identities, but helps them escape, thereby sacrificing his own life in the process. Redemption through sacrifice and forgiveness.
Herzog's version is completely stripped of religious imagery or significance. Instead we see the images of violent nature and chaotic forces common in so many other Herzog films. Where Ferrara's lieutenant sees images of Christ's suffering on the cross, Herzog's sees phantom iguanas and break-dancing Japanese. Where Ferrara's lieutenant "solves" his case by helping the criminals escape and sacrificing his own life, Herzog's sees a bizarre twist in fortune, and arrests his criminals on phony evidence, though preventing his partner from slaughtering them on the spot, instead trusting the due process of law to see right. There is redemption here, but redemption through a combination of chance, diligence, and assistance from others.