The specific details of "why" are themselves subject to much debate by post-war historians; with various historians blaming one side or the other or both. That said, the root of the problem can be traced simply to one issue: Resource allocation.

Japan in the 1930s was not yet a modern economic superpower. It was industrialized but still far behind the United States and the Soviet Union economically. The military budget consequently was very limited, and thus the IJA and the IJN were both constantly squabbling with one another for a bigger piece of this pie.

This was exacerbated by the fact that Japan was facing multiple potential enemies, and both the Army and the Navy had very different ideas on how to resolve these threats. The Army's solution, ultimately, was the conquest of China and to use its population and resources to make Japan into a superpower (the Navy rightly pointing out however that this was impractical - China was too big and had too much population). The Navy's solution, coming from the tradition of Tsushima, was to engage and destroy the battlefleet of their enemies in a "decisive battle" (which the Army right saw as impractical also, because the Japanese battlefleet was smaller than its rivals due to the Washington Naval Treaty).

These were simply not compatible strategies, and with neither side wanting to admit that both strategies were unworkable they feuded with each other incessantly rather than confront reality.

As for during the war itself, the IJA focused primarily in China while it was mainly the IJN which fought the US forces - indeed the IJN had basically developed their own ground units avoid having to ask the IJA for troops for some of the battles.