Yeah the Japs were shit in WWII for a variety of reasons.
1. They went into a form of ultra-nationalism. If you weren't with them and their plans in the military, you were against them and deserved to get fuck. This happened because the military began to take over the actions of the government and lead to literal assassinations and beatings of civilian officials who knew what they were doing.
2. The Japanese constitution calls on a strong Emperor to reign the military in. The Supreme War Council could act independently of the civilian government and answered only to the Emperor.
3. The Japanese was really fucking drunk on victory from Russo-Jap War despite being on the brink of collapse (economically) and the US/Brits saving them. They were also drunk on capturing things from the Germans during WWI and were ass hurt Western Powers wouldn't acknowledge them.
4. The military/government in Tokyo had no control over the actions of its troops stationed in Korea/China/and Islands. The security forces (Kwantung Army) orchestrated the invasion of China and Tokyo had to go along with it. The Army/Navy also got into a pissing contests, acted independently. The Army built its own Navy and the Navy's submarine forces acted as their own branch..
5. Japan never practiced what it preached and encouraged its soldier to put civilians/enemies populace in line. Resulting in atrocities in Nanking and Manilla and PoW treatments and none of the soldiers really got punished.
Japan was a mess from its central government to the operation of its military. Doesn't help that many of the older officers (General to Colonels) didn't want to adapt to new ways of warfare/kept up dumb traditions. One punishment at the naval academy is that you stand under the hot sun for hours while holding two pales of water instead of doing something productive. NCOs would also be able to beat you to teach you a lesson with little accuse.