* At the end of the movie, as the main trio is leaving Archimedes' library behind, Tee argues with Leonardo about whether or not to lead the rest of the Delta Knights to the library. One of the arguments Tee uses is "Remember what happened to Atlantis", implying that the people of Atlantis wiped themselves out with their advanced knowledge. Except it's never stated in the movie (or at least the {{MST3K}} version) what happened to Atlantis. Without that explanation, it just comes across as a weak justification for Tee deciding TheWorldIsNotReady for Archimedes' secrets.
** And this is besides the fact that there's nothing stopping either Leonardo or Thena from saying "Screw you, kid" and coming back with crews to dig the library out.
*** Thena flat out said Tee was right about keeping the storehouse hidden, and Leo eventually burned the map, implying he also agreed with Tee (even if he wasn't happy about it).

* Right before Baydool dies he and Tee refer to each other as father and son. Was this supposed to be in the "like a father to me" sense or was this revealing that Baydool was Tee's biological father?