The NFL refused to correct the false reports that stemmed from league leaks for no apparent reason. This wasn't the case of a single rogue employee, but a potentially coordinated approach by multiple persons because these false leaks stemmed from multiple sources.
The Patriots requested that the "independent" investigation look into those responsible for these false leaks because it would imply that there were persons within the offices that were actively trying to portray the Patriots and DeflateGate in a negative light.
According to a Letter from Patriots lawyer Daniel Goldberg to NFL Genera Counsel Jeff Pash, the NFL requested that Ted Wells not look into the leaks, but instead that the league would investigate on their own.