You Are Already Checked In

A character arrives at a security checkpoint where he has to verify his identity in order to gain entrance. He takes out his ID-card, runs it through the scanner and is surprised to find that it is being denied. The receptionist then tells him that he is already checked in. This can only mean one thing: An impostor is on the loose! Curiously, the guards never seem to suspect the second person/group of being the true impostor.

If the hero is the impostor, it means that his cover is blown, and he must prepare to fight the local security team. If the villain is the impostor, chances are that he has already fulfilled his objectives and destroyed the evidence/killed the witness/sabotaged the equipment, etc.

A variation of this is when the security check is especially high-tech and demands a finger/hand/iris scan. In these cases, expect cloning or time travel to be involved.

Anime and Manga

 * This happens in The Castle of Cagliostro. Unusually for this trope, the imposter is the second Inspector Zenigata to pass through the checkpoint.
 * In what might be the only case of both people involved being heroes, this foils an Impersonation Gambit during the final arc of Princess Principal.

Comic Books

 * The Dark Knight Returns: A detective shows up at a crime scene and talks to Police Chief Yindel. Then he walks away. Then he shows up, coming from the other direction. Yindel points at the departing cop and goes "stop that man!". The next panel is him leaping onto the Batcycle.

Film

 * In The 6th Day, Adam Gibson uses a finger from a dead clone to gain entrance. He is discovered when a new clone with the same fingerprint tries to check in.
 * Multiple people in The Fifth Element try to check in on the Fhloston Paradise with Korben Dallas' identity. It becomes something of a Running Gag.
 * Subverted in Sneakers. Werner Brandes (who has a genius-level 180 IQ) knows that someone has stolen his ID card with the intent of breaking into the place where he works, and there's a (repeatedly shown) paper printout of who has entered and left the building. However, when he gets there he doesn't ask the security guards to check the entry/exit register and see if "he" is listed as still being inside the building, which would prove he's right about the break-in.
 * Ultraviolet: After Violet pretends to be a courier in order to sneak into the Arch-Ministry building, the real courier shows up and her ID is rejected, thus alerting the guards.
 * Sort of happens in The Last Action Hero. The fictional villain "The Ripper" shows up to a movie premiere (of a later movie in the same series) and is briefly interviewed by a reporter, who thinks it's Tom Noonan (the real-life actor) dressed up as the villain. Then, the real Tom Noonan appears, dressed as himself, confusing the heck out of the reporter.
 * In From Paris with Love, the assistant to the American representative at the conference gets this, even though he's the real guy. The person who used his ID before was.

Live-Action TV

 * Used in Supernatural: The brothers check into an evidence warehouse using Homeland Security IDs, but are forced to flee once some very serious suits from Homeland Security arrive at the desk.
 * A comedy variant: On Mad About You, Jaimie was going back to school, but Paul had forgotten to send in her registration forms. So he, Ira and Jaimie's friend Fran stealth sign her up for all the classes she wanted on the last day of registration, getting signatures from the teachers of the classes in question, and all had to get photo IDs taken, claiming they were Jaimie Buckman.
 * Happens in the miniseries The Last Enemy, when the protagonist needs to talk to somebody being held in a secure medical facility. A fingerprint scanner is involved (but no cloning or time travel—it's pointed out that current fingerprint scanners really aren't that hard to fool).

Video Games

 * A variant is used in The Legend of Zelda: Majora's Mask. Link is shocked to discover that a room at the Stock Pot Inn has already been reserved for him. Turns out there's a Goron also named Link who made the reservation. You just happened to arrive before he did. Steal his room at your peril, 'cause you can find him outside shivering in the cold later if do. Remember that this is the festival season, and all the hotels were booked solid a long time ago.
 * The Goron doesn't get angry if you steal his room, though: if you do so, his Verbal Tic makes him say his name as "Link-goro!". The receptionist doesn't understand him and sends him away saying there's no reservation under that name.

Western Animation

 * In the League of Super Evil, this went along with the Totem Pole Trench gag.
 * Family Guy: Meg's getting married, Neil Goldman isn't invited but wants in. Chris is checking at the door. After giving his real name and being rejected, Neil says he's Chris, who immediately switches places w/o question. When Chris gives Neil his name, he's told Chris has already checked in.