Maybe it was in a TV version? Or a comic book, or script? Or, just a Cinematic Urban Legend (a phrase which I just coined)
Yep - it's a good 'ol CUI.
I first heard of this rumoured scene about 8 years ago when reading message boards. From that point it's just kind of gathered steam.
I've read the final draft of 'Raiders' which still included the Nazi with the robotic arm, but there is no hint of a scene with the burning crate at the end.
I think this could come from school yard talk, you know, those kids that swear they saw it just because they imagined or dreamt it.
It wouldn't make any sense in context, besides. The whole point of the last scene is that the Ark is added to the warehouse, where there are literally tens-of-thousands of mysterious artifacts and dangeous items. The Ark is just one more of them, and, as Indy says, the fools "Don't know what they've got there."