When Marshall is describing the best burger, he says that the buns have sesame seeds. However, when they finally find the "Best Burger in New York," the buns are seedless.
During the opening, a reference is made to the Elbow Room (an old punk rock club), which became a drug store. What really happened is that the Kim's Underground and the former Elbow Room (not a punk rock club) at 144-146 Bleecker Street, became a Duane Reade drug store in the Spring of 2006. The image shown purporting to be the Elbow Room is really a club from across the street (The Bitter End) and Terra Blues, both with the signage on their marquees digitally removed.
When they are trying to decide a place to eat, and Barney says "I hate Chinese food." Back when Lily was stabbed with the wall decor swords, they all went to eat at Lily's old apartment that was turned into a Chinese restaurant.