A. When the bills defender hit the jet player on the sideline, he bobbled the ball as he was going out of bounds. The officials ruled this as a loss of control the ball, which is very very subjective in the rulebook, so the fact that he got both feet in bounds doesn't matter. It's a little bit of a ticky tack call, brought to you by an officiating crew that makes ticky tack calls. The other note here is that if there's any question whether or not it's a completion, a pass is going to be ruled incomplete.
They generally don't call the penalty for throwing a challenge flag on a reviewed play anymore and the NFL has expanded Booth reviews this year. So it was either reviewed because it was a change of possession as you said, or it was reviewed as part of the NFL's new expedited replay review, where are the replay office basically reviews any play that's close and radios in. Officiating Crews use the words after discussion on the field in that situation in particular.
B. On a penalty during a run play, defensive penalties are enforced at the end of the run. Think facemask, horse collar or hands to the face.