There is no question the investigations and prosecutions of both Avery and Dassey were flawed. The incompetent representation of Dassey by Len Kachinsky likely had a significantly deleterious effect on both cases.
There are a number of pieces of evidence that cause me to have real questions about whether Avery and/or Dassey were guilty. In particular, the recorded calls of Avery talking to his fiancee the day of the murder - he sounds unhurried and calm - and the recording of the Manitowoc officer calling in the license plate from Teresa Haibach's car, days before it was found.
All of that being said, the film is told with a significant pro-defense bias, and in some ways it presents the evidence in what I consider a somewhat misleading way.
I have read the transcripts of the interviews of Brendan Dassey - they are at
http://www.convolutedbrian.com/dassey_confessions_links.html (I have not listened to the audio or watched the video, however). To me the questioning is not unduly suggestive as a whole, and there's no question he is the one who originates much of the relevant information. In places he has included corroborated, incriminating details that were never referenced in the movie (e.g., he states that he and Avery put the car by the pit on the property, and Avery covered it with sticks and a car hood, which was in fact the way it was found, and he also states that Avery put the body in the car before deciding to burn it - this would account for the presence of bloodstains in the back of the car consistent with her bloody head touching the interior of the cargo area of the car). He also refuses to agree to certain things that are suggested by the detectives (e.g., he is adamant that he did not shoot Teresa Haibach despite being asked repeatedly whether he did). Certainly if I had conducted this interview I would be left with the impression that he was telling the truth. I was also troubled by the trial testimony by the female cousin, who told the authorities in March that Brendan had lost weight and seemed really upset for months after Halloween, and told her about the body being in the fire. I know she recanted at trial, but I thought this was still a fairly persuasive piece of prosecution evidence.
I find it hard to analyze the question of whether Avery and Dassey are guilty without having seen the entire trial, or learned more about whether there was any plausible alternative suspect. I frankly don't believe the police committed this murder, though I could certainly imagine them tampering with evidence. I know the defense was barred from naming anyone else as a potential suspect, but I gather they also really didn't have one, or the filmmakers would have referenced that. I know Teresa had received the unwelcome phone calls, but given how thorough Avery's attorneys were, and the fact that they had access to her cellular phone records, I assume they ran that lead to ground and it didn't point to a viable suspect. Based on that, we are left with the fact that the murder happened on the Avery property, and he was the last person known to have interacted with her.
Overall, I think it's likely (though far from certain) that Avery is guilty, and I would not be shocked if Dassey is as well. That being said, I think there was reasonable doubt with respect to both cases, and that they should probably not have been convicted.