As much as I do feel there was some type of tampering going on ( I'm not even sure it happened at the AFCCG) the Patriot's do have legitimate gripes in how the whole incident has been handled, here is a list, the worst one is when the official tells them (Well's) what gauge he used pre-game on the Patriot's balls but they refuse to accept it because it would mean all the Pat's balls fall into the "unmolested" category and hey, 5 mil is a big chunk of change so we're not going for that bro so we will just declare your 'best recollection" fine EXCEPT when it makes our report look wrong.
Incorrect communication on PSI. In a Jan. 19 letter to the club the day after the AFC Championship Game, senior vice president T. David Gardi wrote that an investigation was starting and one of the footballs measured at 10.1 psi. In the letter, Gardi wrote that each Colts football that was inspected met the requirements. That information was incorrect or incomplete; no football measured at 10.1, and three of the four Colts balls measured below regulation on one gauge.
Acceptance of Wells report's interpretation of certain data and rejecting Walt Anderson's recollection. Referee Walt Anderson recalled that he used the "logo gauge" for pregame measurements, which would have meant the total average of all Patriots footballs were in compliance at halftime. But the Wells report rejected that recollection, while accepting it for the measurement of Colts footballs. It was the lone recollection of Anderson that was rejected. The NFL did not challenge this interpretation, which was a central part of the Patriots' rebuttal website, Wellsreportcontext.com site (Paragraph 5 of executive summary).
Media leaks, culminating in Tuesday's regarding Tom Brady's cell phone. Kraft expressed his outrage at the Super Bowl with various media leaks from the league office that contributed to shaping public perception, which was also reflected in a February communication with NFL general counsel Jeff Pash. The issue continued right up until the hours in which the NFL announced the decision to uphold Brady's four-game suspension as information about Brady's cell phone being "destroyed" was reported by ESPN.
Portrayal of "destroying" cell phone. As Brady noted in his Wednesday statement, he had told league officials that under no circumstances would his phone be subject to any part of the investigation, which is his right as a union member.
"To suggest that I destroyed a phone to avoid giving the NFL information it requested is completely wrong," he said.
Kraft also blasted the NFL on Wednesday for how it portrayed Brady replacing his cell phone
Suspension of team employees. In his 20-page opinion upholding Brady's four-game suspension, Goodell notes that the Patriots informed him that they suspended equipment assistant John Jastremski and officials locker room attendant Jim McNally. That is technically correct, but it's my understanding the decision was made after consulting with the league and top NFL officials, who essentially said, "Are you going to suspend them or are we?" So it's my understanding that was as much a joint decision as anything.
Accountability. In March's annual meeting, Goodell said that if the league did anything wrong as part of its investigation, it would be reflected in the Wells report. The 243-page report included one paragraph on the topic (Page 21, executive summary). There has been no other public acknowledgment of missteps. That helps explain why Kraft, in his statement Wednesday, said: "There are those in the league office who are more determined to prove that they were right rather than admit any culpability of their own or take any responsibility for the initiation of a process and ensuing investigation that was flawed."