When the alarm clock goes off, Alice knocks it to the second shelf (at around 1h 35 mins). Alice goes back to sleep and some short time later, without either her or Tommy having moved in the bed, the alarm clock has returned to the top shelf of the nightstand.
When Alice and Tommy first see the "Leaving New Mexico" sign, the traffic light they are approaching turns from green to yellow. Following a very brief exchange inside the still-moving car, the light is then shown to be green, and they go right through the intersection without having slowed or stopped. There was no time for the light to have gone through a full cycle.
Tommy says the A7 chord hurts his fingers. A7 is one of the easiest chords, even for beginners. Kristofferson would know this and could have asked the script be altered, and recommend a more difficult chord.