Right after we see Shane in the beauty supply store helping Rory and Lane, we find out that she was in the closet in Luke and Jess's apartment. Later that same day, she is still back at the beauty supply store, talking to Jess about what time she gets off work. She couldn't have been at work and in the closet at the apartment at the same time.
When Lane and Rory leave the beauty store, they are both wearing different clothes than when they're in Lane's house, even though it's supposed to be the same day. Shane is also wearing a different outfit when Rory and Lane buy the stuff to dye Lane's hair than when she's talking to Jess on the phone and Rory yells at her.
When Lorelai and Rory are cleaning out the garage, they find the Hug a World pillow which is worn and faded. Rory alludes to the fact that she hasn't seen it in years, however in the previous season, when Rory returns from her picnic with Jess, it is seen on the couch looking brand new.