Blooper: In a season 6 episode, Rory tells Logan that she lost her virginity to him, when the one she lost it to was Dean. Of course, it's not impossible that she lied to make him believe he was her first, but she doesn't seem like the type who would.
Channel Hop: A demented example when the series was screened in Britain; the first three seasons aired on Nickelodeon of all places (and were prone to being censored and have episodes dropped), with the Hallmark Channel picking it up and premiering seasons four and five, before E4 gave the final two seasons their UK debut (and ultimately screened all seven).
Heavily in season six, and once Amy was out the door, very apparent in season seven as the show was used basically by the CW in order to trap viewers into sampling the other awful wares of their inaugural season without regards to six seasons of well-established continuity or writing by such luminaries such as Jane Espenson.
The new executive producer who came on had some odd baggage, having been slapped with a restraining order by Heidi Klum (his co-worker when he wrote on Spin City) after he wrote a bizarre and offensive one man play performed in New York about how he'd really, really, really like to sleep with her, after which he was involuntarily committed for a spell by his father. Thankfully he left the Girls alone...physically. Characteristically however...
Dean coming back and having his affair with Rory, pretty much so that the network could remind their audience that Jared Padalecki still was there and ready for Supernatural, coming to the WB Thursdays next fall!
Hal Douglas, the voice of the WB, didn't move over to the CW, thus the show lost their authoritative Father Figure promo voice, replaced with an unknown voiceover artist who you saw more describing the wacky hi-jinks of the earlier double-shot of Everybody Loves Raymond (tonight at 6:30 on CW67!) than working as the Danny Dark of the fifth network. It also sadly proved that the brain trust at UPN rather than the WB was in charge and didn't know what to do with a successful series.
Nickelback playing in the season seven promo teasing the infamous 'Wedding in Paris' episode. Nickelback is a band that would never go near Lane or Rory's CD players, and Top 40 music was only mentioned in derision or as a necessary evil in the background of dance scenes during the AS-P era.
The cast photos for season seven playing up Lorelai, Rory, Luke and Logan wearing way too much spray tan at the expense of the rest of the entire cast, which didn't get one picture. Again, UPN thinking (as earlier cast photo shoots involved all of the stars and sane photographers).
The continued employment of David Sutcliffe, who only came back in the later seasons after failing as the lead guy in I'm with Her, an ABC sitcom with Teri Polo which happened to be scheduled against Gilmore Girls and was beaten in the ratings by it a few times.
In-Universe meddling was performed by Terrance, Paris and Paris' dad to set Paris and Rory up as roommates at Yale.
Fake Nationality: Lane Kim, Rory's Korean best friend, is played by a Polynesian actress. Lane's mother, Mrs. Kim, is also played by a Japanese-American actress.
Reality Subtext: Rory and Jess shared a good lot of on-screen chemistry. This was likely due to their actors dating in real life.
Romance on the Set: Milo Ventimiglia (Jess) and Alexis Bledel (Rory). They met when he was cast as Jess and remained together until separating in 2006. As mentioned above, it lends quite a bit of Reality Subtext to Rory and Jess' final scenes together.
Mia, the owner of the Independence Inn and Lorelai and Rory's surrogate mother/grandmother was played by a different actress in season 7.
Cesar, one of the servers at Luke's Diner was played by a thin, tall Latino actor in the first two seasons, but was only really ever in the background and never had any lines. In the later seasons, Cesar was played by Aris Alvarado, who was chubby and didn't really look anything like the first, but he became one of the town's quirky characters and had the rare scene every once in a while. Viewers could be forgiven for not noticing the change.
Screwed by the Network: Might as well be renamed Screwed by Dawn Ostroff. The WB let Amy do whatever she wanted for six seasons, but once somehow Dawn became the leader of the new CW instead of any one of the WB's competent executives, the show started its stunning death spiral towards the last half of the sixth season, and her meddling with the show to use it as part of a Bait and Switch strategy to make viewers forget completely about the well-loved WB and forget UPN ever existed alienated most of the fanbase outside of the Rory/Logan shippers. And even that small win was destroyed with the abrupt series finale where they were broken up. Both Liza Weil and Kelly Bishop (who both rarely speak ill of anyone or anything in their careers) expressed disgust publicly that a proper series finale wasn't filmed as a Plan B in case of cancellation.
What Could Have Been: Sookie was played by Alex Borstein in the unaired pilot, but she couldn't dedicate her time to the series proper because of her commitments to MADtv.
Jess was supposed to appear in the final season, but Milo Ventimiglia refused when Amy wasn't the director anymore.
Emily Gilmore's jewelry is actually Kelly Bishop's own jewelry as she is allergic to the nickel plating used on costume jewelry.