From the judge's ruling in the case:

Both Dr. Coates and Dr. Schultz expressed their opinions that Mr. Allen did not sexually abuse Dylan. Neither Dr. Coates nor Dr. Schultz has expertise in the field of child sexual abuse. I believe that the opinions of Dr. Coates and Dr. Schultz may have been colored by their loyalty to Mr. Allen. I also believe that therapists would have a natural reluctance to accept the possibility that an act of sexual abuse occurred on their watch. I have considered their opinions, but do not find their testimony to be persuasive with respect to sexual abuse or visitation.  

I have also considered the report of the Yale‐New Haven team and the deposition testimony of Dr. John M. Leventhal. The Yale‐New Haven investigation was conducted over a six‐month period by Dr. Leventhal, a pediatrician; Dr. Julia Hamilton, who has a Ph.D. in social work; and Ms. Jennifer Sawyer, who has a master's degree in social work. Responsibility for different aspects of the investigation was divided among the team. The notes of the team members were destroyed prior to the issuance of the report, which, presumably, is an amalgamation of their independent impressions and observations. The unavailability of the notes, together with their unwillingness to testify at this trial except through the deposition of Dr. Leventhal, compromised my ability to scrutinize their findings and resulted in a report which was sanitized and, therefore, less credible. 

And interestingly, Dr. Leventhal himself never met with Dylan. I believe the Connecticut Magazine article goes into how the Yale-New Haven study was flawed.

But despite all this, including the judge's serious concerns about the study, Woody Allen had no problem touting it as vindicating him, the same way he and his defenders have no trouble claiming he passed a polygraph, without mentioning that he refused to take one from the police and instead "passed" the one that he took privately and paid for. 

And this (and there's still much more to read in that opinion):

Mr. Allen's deficiencies as a custodial parent are magnified by his affair with Soon‐Yi. As Ms. Farrow's companion, he was a frequent visitor at Soon‐Yi's home. He accompanied the Farrow‐Previns on extended family vacations and he is the father of Soon‐Yi's siblings, Moses, Dylan and Satchel. The fact that Mr. Allen ignored Soon‐ Yi for ten years cannot change the nature of the family constellation and does not create a distance sufficient to convert their affair into a benign relationship between two consenting adults.  

Mr. Allen admits that he never considered the consequences of his behavior with Soon‐Yi. Dr. Coates and Dr. Brodzinsky testified that Mr. Allen still fails to understand that what he did was wrong. Having isolated Soon‐Yi from her family, he left her with no visible support system. He had no consideration for the consequences to her, to Ms. Farrow, to the Previn children for whom he cared little, or to his own children for whom he professes love.  

I knew a lot about this case and Woody Allen, but have learned still more recently, and all I've learned demonstrates to me that he's a liar without a conscience and concern for others. The judge wrote at length about how he's self-absorbed and seems to lack any true consideration for the well-being of other people, and gave many examples of how that's so. And about 25 years later, those same sorts of things were evident in this interview he gave:

https://www.huffingtonpost.com/entry/woody-allen-is-creepy-af-about-soon-yi-in-the-hollywood-reporter_us_572a39e4e4b016f378946e02

Oh, and the judge's opinion addresses the major points of the pro-Allen testimony given by Dr. Coates which the old NY Times article is about.