Berkeley applied for a patent on tennis balls, an application still pending. Harvard/MIT later applied for a patent on yellow tennis balls and paid a fee to accelerate the review of their application. The Harvard/MIT patent was issued first. The recent PTAB trial found that the Berkeley patent application did not interfere with the Harvard/MIT patent, but this does not mean that the Berkeley application will not issue, nor does it mean that one could practice yellow tennis balls (CRISPER/Cas9 in eukaryotes) without licensing both from Berkeley and Harvard/MIT.
As to how Harvard/MIT won, part of the PTAB decision relied on general statements made by one of the Berkeley inventors as to the challenges in dyeing tennis balls yellow (getting the CRISPER/Cas9 system working in eurkaryotes) and so demonstrating that the Harvard/MIT inventors had to made an inventive step. That is a pretty profound and worrying development with respect to academic freedom.