OK, I only listened to the final episode last night. I'm another one putting Jay right in the frame and the reason I think he got away with it is that he is black and Baltimore is an overwhelmingly black city. A lot of the jurors were black and, as per the episode in which SK interviewed some of them, they liked the way he came across during trial. Adnan, on the other hand, was surrounded by "scary, beardy" Muslims (SK also mentions that a ton of supporters from the mosque turned up to the trial) and, despite it being pre-9/11, they quite possibly had their own prejudices about Pakistanis and south Asian Muslims.
And Adnan didn't testify. So they had a nice young man trying to be helpful to the prosecution and being harangued by the defence barrister up against this more unfamiliar young man who is surrounded by suspicious types and won't even speak up in his own defence. That doesn't explain why the police were so ready to go with Jay but I think it might help explain why the jury were willing to overlook the (many, many) holes in Jay's evidence.