- Alternative Character Interpretation: In the Florence episode: Did Puccini successfully sweep Anna off her feet during the week her husband was gone, or was it a combination of harassment and guilt-tripping on his part that made her feel she had to go with him? Many fans accuse her of the former, but her Broken Tears over the issue (and belief in Puccini's statement that he "cannot create" without her as his muse) seem to point toward the latter.
- Bizarro Episode: "Transylvania, January 1918". It comes out of nowhere and even years later still makes no freakin' sense. (In the original, never aired cut, the Transylvania episode was told as a ghost story by the old Indy to some children in Halloween. So there was the possibility that it was completely made up. But then the new cut had to screw it completely...) It does, however, feel closer in tone to the movies which often have supernatural shenanigans and goings on.
- Complete Monster: Mattias Targo, from "Masks of Evil", is a bloodthirsty Romanian general and a literal vampire all but explicitly stated to be the reincarnation of Vlad Tepes himself. Targo liberates an Austrian P.O.W. Camp solely for his own ends, murdering dozens by turning them into members of his vampire army and keeping them trapped in undeath, and killing many more by having them brutally staked all around his castle. Targo murders three foreign spies sent to investigate his affairs, sending their body parts back to their superiors, and when Indy and his allies break into his castle, Targo kidnaps them all with gruesome designs for them. Targo tortures one of Indy's allies to death by horrifically vivisecting him alive and screaming with similar intent for Indy and his other friends, after which he intends to have his army sweep through Romania and cleanse it in a wave of blood, slaughtering all those he decrees "intruders" onto his land.
- Fanon Discontinuity: Some fans of the movies prefer to ignore the TV series. However, the re-cut of the series (which does away with the frame story that causes most of the tension) has been better received.
- Growing the Beard: The Sean Patrick Flanery episodes are able to be have more varied plots, greater stakes, and more character development than the Corey Carrier episodes. The Carrier era is also repetitive, since its plots largely revolve around Indy running off and having mild conflicts with his dad.
- Hilarious in Hindsight: One episode involves Indy hunting down something known as The Phantom Train.
- Retroactive Recognition: Episodes featured then unknown actors Elizabeth Hurley as Young Indy's British suffragette girlfriend, Catherine Zeta-Jones, future James Bond and Felix Leiter Daniel Craig and Jeffrey Wright (in different episodes), Jane Krakowski, Anne Heche, Douglas Henshall from Primeval and Clark Gregg (aka Agent Phil Coulson in the Marvel Cinematic Universe). Even Young Indy himself, as most know Sean Patrick Flanery from The Boondock Saints nowadays.
- Special Effect Failure: Oh, so much. Granted, it was made in the early '90s, but still...
YMMV / The Young Indiana Jones Chronicles