I think it would be fair to say that Antonio Allen is struggling a bit at cornerback. It's not his fault either. He has never played the position before. When players change position, they usually at least start making the transition in the offseason so they can work in OTA's, have a full training camp, and do plenty of time studying. Allen was moved on the fly during the preseason, and an injury made his time even more abbreviated.
Just from watching him, he really doesn't have a great feel for the position. You could tell that on the timing patterns the Packers hit Sunday. You could tell it when Allen was flagged and didn't look for the ball. I think the final play from scrimmage before the Packers went into the victory formation is probably the best indication of how much Allen is a fish out of water right now.
The Jets are out of timeouts with under 2:00 left. A Green Bay first down ends the game.
Note where the first down marker is and the cushion Allen gives Nelson on this pattern.
Again, I don't blame Allen here. The Jets are hanging him out to dry on this cornerback thing when he hasn't really had a chance to learn the position at all.