IMO, it does not necessarily have to be incompetence and/or dishonesty. Many times LE and/or prosecutors get so attached to their own theory that they have blinders. If they even see evidence that suggests their theory is wrong, they find an excuse to dismiss it.
A great example of this is the movie "The Interrogation of Michael Crowe." It shows how LE and even DA's can be so attached to their theory of the crime that they are blinded to any other possibilities. The theory was formed because a 14 year old boy did not show the emotion over the death of his sister that they felt he should. Even when DNA evidence linked a transcient to the murder of a 12 year little girl, they still refused to accept and/or believe it. The State's Attorney finally stepped in to take over the case.
So yes, even with other LE agencies involved, they can get attached to a theory to the point of overlooking and/or denying evidence that goes against that theory.
I want to give a small example of something that pertains to what you wrote. My daughter got in trouble with her ex bf-family violence. He started the fight, hit her 1st, beat the crud out of her, but she fought back. She called 911 for help, because when another girl intervened, he started choking her. My daughter then called me & I also called 911. When the cops got there, they talked to the homeowner, (the ex's friend), & he said my daughter 'playfully' slapped the ex 1st. They did not interview the other girl. They wrote on the report, that my daughter was the aggressor, & arrested them both. They wouldn't listen to my daughter, & treated her like a bully & a liar. She's 5'5 & 115 lbs, the guy is 6'0 & 185. She had a crack in her skull, black eye, busted cheek bone, etc...but they said she shouldn't have fought back, just called them. & in the picts, he did look more damaged...but it was because the other girl had busted a bottle over his head...but they wrote in the report, that my daughter inflicted it all. The cops called her bad news & reccomended to the ex that HE stay away from HER. Well, the charges did get dropped, but after talking to the assistant DA, he said that because of the report, he'd have a better case of winning for the ex instead of my daughter...even though on the 911, you can clearly him him beating the crap out of the other girl, her begging for help, him raging at my daughter, & knocking the phone out of her hand, & choking her. & the reason is because...when he screamed at her, 'who are you calling, *****, the cops?', she didn't say yes. So, no 911 interference. Also, on the report, the cops wrote that the other girl called 911...the girl they earlier claimed wasn't even there. My call wasn't even factored in, & I clearly stated that she had just called me, after calling 911. So, the cops made a mess out of the report, & IMO, the DA didn't want to call them on it. I do believe that my daughter would've beaten the ex in court, but in reality, we were nervous about 'going there' against the cops. We just decided to let it go. Also, after being arrested, the ex was so out of control & violent, county had to strap him in a restraint chair. The police report said that they were both drunk, but the county reprt, (less than 30 mins later), said that he was drunk, & under the influence of drugs, & my daughter was sober & cooperative, but visibly upset. So, to make a long story short, I don't think our city cops, DA, etc...are corrupt, but I do think that once the ball gets rolling, with that initial report, everybody else just follows in a line, to support it. But, I do think cops need to learn how to assess situations better, & it'll be a cold day in ****, before we ever ask them for help, again.