My understanding is that Newton was declared eligible in the summer, by all parties, then new information surfaced which was investigated further in November.
He was declared ineligible when the NCAA informed Auburn that there were possible violations not previously known. The NCAA immediately cleared him of eligibility issues and so he played the season out. If, in the future, violations are found to have occurred then the NCAA could reverse their decision. The eligibility department ruled him eligible. The infractions group is still investigating, though they are likely just waiting to see what, if anything, shakes out of the Louder and McGregor trials.