That's not true. Wells said that the League didn't take the allegations seriously. This who charade is 100% on the league. It could have blown over with a statement of, "We'll look into it." The NFL let it happen.
Then, because they went through this ridiculously overblown investigation, they had to place blame. The investigation was not independent, nor unbiased. Wells' only marching orders were, "Protect the Shield," which means no blame on the NFL or the Referees (Imagine the Integrity of the Game charges otherwise?). Obviously, the equipment managers were getting the ax, but they are small potatoes. Again, imagine if the NFL spent in excess of $1 million for a sham report only finding fault with a part time ball boy? That leaves Brady as the only party of consequence. The $1 million fine to the Patriots (ownership, GM, and coach of which were found to have zero knowledge of the goings-on) was only so the NFL could cover it's costs paid to Wells' law firm. Ironically, the Patriots make out in the deal because they get to withhold $2 million they would owe Brady for the 4 game suspension (that will never stand up. It's getting reduced to 2).
Be that as it may, had the NFL gotten out in front of it, this whole ordeal would have resulted in a small fine. Instead, they have egg on their face.