At the end when Emily enters the diner, Luke asks Kirk if he wants coffee. Kirk says that coffee makes his lungs hurt, but in other episodes, Kirk is seen drinking coffee and asking for refills multiple times.
When Lane visits Rory at the bookstore, the same couple approaches the magazine rack outside the door four times.
When Emily & Richard are talking in the kitchen, after Emily cuts the Irises , the Irises change with each shot of just Emily. At one point there is a tall Iris on the right, the next they are all around the same height, then it looks like there are more Irises, then the vase is missing all together, and then it's back and less full.
(at around 5 mins) Behind Lane you can see a man and a woman, in a white coat, walk towards the bookstore, the woman is seen picking something up.
Later (at around 16 mins) the same action happens again.
When Lane is talking to Rory in the bookstore, through the glass door you can see the same couple stoops down to look at the magazines four times.
When Logan helps Rory pick up her dropped money, he refers to it as a "cute meet", but the actual term is a "meet cute".