While Indy and Sophia are looking for Atlantis after hiring a boat on the fists path, Indy puts on a diving suit and Sophia switches on the air compressor. If you select "pull switch" while the compressor is running, Sophia will say "It's already on." with Indy's voice.
At the hotel in Monte Carlo during the team path, when the lights are turned off in the hotel room, if you click "Use Bedsheet" while Trottier is not in the room, Indy will say "Now is not the time" in Sophia's voice.
On the wits path, the Nazi sailors are in the stern torpedo bay after Indy starts a fire. If you take Indy up to the conning tower and use the "look" command on the lower deck, Indy says that he sees a couple of Nazis down there when there are no Nazis in sight, as they are in the stern torpedo bay.
When explaining how the Greeks discovered Hyperborea, Dr. Heimdall claims they traveled "thousands of miles." By 1939, Iceland had adopted the metric system, Therefore, Heimdall should have meant "kilometers", instead.
During the game's climax, when Indy and Sophia (regardless if she was rescued from the dungeon or not) are in the air lock to escape Atlantis, heading to the submarine, if Indy leaves behind the ladder on the steep rocky incline, the ladder will be gone at the end.
Indy can leave the stone box, which contained the light wand to light up Atlantis open or closed. If it's left open, it will be closed at the end of the game when Indy and Sophia (whether she's with him or not) are escaping from Atlantis.
The CD-ROM version contains a bug: On the Team Path, if Indy climbs down into the Nazi submarine without distracting the crew, one of the sailors will spot him, and say "You there!" (according to the screen text). Instead of replaying a voice sample, the game will emit loud, noisy static.
When Indy asks Sophia if she "found Nur-Ab-Sal" after she falls in the hole at the dig site, she says "you're dead meat!" twice to Indy. However, the screen text censors the phrase "dead meat", implying that Sophia says something a little nastier, both times.