This is a known bug caused by pressing the loot all on the chest instead of manually clicking and dragging the item from the chest. I'm glad to hear that you figured out the known work around!I've reached the sky portion of Temple of Ra but instead of having an exclamation mark there it was just the thing with (...) dialogue. Is this a bug or did a miss something? I got the bottle and the Relic.
Every shortcut after the place you get the bottle also did not open so it makes me think a script got stuck somewhere.
EDIT. Fixed it, apparently the trigger was stuck on the chest you get the bottle, I trashed the one I had and got a new one and the exclamation mark was gone. Can't say I know what caused it.