How about the submarine bit in Raiders, and Last Crusade has plenty:
The entire opening sequence, with Young Indy acquiring his whip and whip skills, his chin scar, fear of snakes, love of adventure and his fedora all in one afternoon and in the over-the-top manner it all occurs.
The plane explosion in the tunnel, which should've not only completely engulfed the interior but also caught the car in the blast radius.
Indy somehow managing to avoid falling with the collapsing tank and making it to the ledge of the desert plains. Okay, so he grabbed at the vines offscreen, plausible enough explanation, but still.
The Grail Knight. For me this is the single biggest WTF? moment in the series. A Knight who's been guarding the grail for hundreds of years and has survived without any sort of nourishment and presumably has just simply stood guard all that time.
None of this is enough to make me dislike the film or think any less of it, mind you. But I find it unfair that TOD and KOTCS get picked apart for their unrealistic moments when the other films also have plenty.