I am not an expert, but my guess would be different priorities with their very limited resources. Why did they have to use 600,000 horses to move supplies along with mostly "stolen" trucks from countries they invaded to invade the USSR? Why did they not recognize the need for spare parts for the stolen trucks and their own tanks would be required when crossing a territory as large as the Soviet Union? Why did they wait so long to start trying to build more subs?
Lots of questions and the only answer I can come up with was different priorities and limited resources.