The Japanese were also horrible at basic tasks like damage control. The USN leaned from the loss of the Lexington & the heavy damage incurred by the Yorktown that once you fly-off your strike aircraft, you drain your fuel lines, fill them with inert gas, to minimize any secondary explosions. Contrast that with the Japanese at Midway... ordnance strewn around the decks, fuel lines strung out...
The Yorktown, as damaged as she was, absorbed an enormous amount of damage at Midway. Indeed had a IJN sub not snuck in while she was under tow, she might have survived and made it back to Pearl.
I believe that they were arming their planes for a second strike on Midway, when an American carrier was sighted.
They then started switching to ordnance for attacking ships, and left the general-purpose land bombs on the decks until they could be stowed later.
Whoops.