The play that bugged me last night was not when Rex Ryan called timeout on the 4th and 1, that happens. It also was not the defensive holding penalty on 4th down, unfortunately, that was the right call. The play that bugged me was on the 4th and 1 right after the Ravens timeout, the Patriots jumped (false start) and the Ravens still stuffed the Patriots. Yet, because it was a false start, the Patriots got moved back 5 yards, and converted on the next play.
I think the rule should be changed where the 5 yard penalty isn't whistled dead (or attempted to be whistled dead) immediately, and the 5 yards is optional, like illegal procedure, illegal formation, or illegal motion. That way the defensive team isn't penalized for stopping somebody, but having to replay the down and give the offense another chance to convert.