A good portion of it was related to logistics and time. The Germans vastly underestimated the entire amount of logistical strain and time that crossing one of the largest countries on Earth would take.

At the start of Barbarossa, the Germans had a standard for distributing fuel called a V.S. (the non-abbreviated term escapes me). A single V.S. was supposed to be enough to get a single Panzer or mechanized infantry division about 100km. While it was pretty accurate on the hard earth and paved roads of west Europe in France or Belgium, it was hardly close in the mostly unpaved Russia. A V.S. from the outset of the invasion was closer to getting these divisions around 60-70km, far short of the desired range.

On top of that, this was further worsened by the fact the trucks delivering the fuel used more fuel themselves, and the fact that Russia was so poorly paved meant that armor divisions often got bogged down, and the supply lines suffered just as much. It got so poor to an extent that horses and pack mules began increasing in usage again just so they could keep moving.

And just to top it off, Hitler had planned to take Russia before winter set and stopped all combat. When that didn't happen due to all the reasons, it settled into a war of attrition that Germany could never win.

Leading up to that point though, the Germans also underestimated the mechanization and technology of the Russian military. At the onset of the war, typical Russian weapons consisted of the standard bolt action Mosin and the PPSH-41. PPSH's are worth mentioning since they're one of the more rugged and major stamped steel weapons, which greatly increased the production capability and allowed them to be turned out much faster. On top of that it was just an extremely well built weapon that was well suited to hard-knock life of front line infantry. Even the Germans valued these weapons so much to where limited production runs of 7.62x25mm were run and there were conversion kits developed to convert it to the 9x19mm.

One of the largest pieces was also their armor. The T-34s and KVs completely blindsided the Germans due to poor intelligence and a general lack of interest of thinking they needed to know. Germans were under the impression the Russian standard was still the BT series and the T-26 series. While they were extremely common around the start of Barbarossa and fared pretty poorly, they masked the more powerful, newer tanks. Despite these tanks being poorly lead most of the time and using dated, interwar, breakthrough tactics, even in less than optimal usage they could still wreck havoc on German armor. There's plenty of stories of Russian armor doing so in a phenomenon rarely seen elsewhere during WW2 called tank shock where the mere presence of advancing tanks could cause mass panic and retreats among the Germans. Until January of 1942, the only ways the Germans had to actually disable those tanks was call in air support, bring 88mm flakcannons to the front, bring artillery pieces to the front, or disable the tanks via jamming the turret rings, blowing off the tracks, etc. While it got the job done for the Germans, with other divisions like the Czechs or Austrians who also fought in Barbarossa, and were only equipped with tanks such as the Skoda 35/38 and other inter-war designs with no heavy artillery or heavy flak, they were utterly demolished by Russian armor.

Another major point was they didn't expect Russia to be able to recover losses so quickly. While Russia had 0 chance if they continued in sustaining losses like they did in 1941, they still had massive reserves of fighting people across the country and the potential for massive production capability. At one point, Stalin personally ordered that no series modifications were to be made to things such as the T-34s until the situation had stabilized across all the fronts, and instead to tell factories to focus on churning out as many tanks and weapons as possible which lead to the seemingly inexhaustible amount of resources that Russia had.

While I can't speak in detail about it, Russians have always been a very prideful, very nationalistic group of people and the ability to keep soldiers morale high wasn't extremely hard when many wanted to fight. Hopefully someone can touch more on Russian propaganda and recruiting during the war because it was a massive effort I don't give justice too.

On top of that, back to Germans, the Germans just didn't have the gear they needed and what they did have was not fit for Russia. German vehicles with thin, 300mm (almost 12") wide tracks or narrow road wheels typically got bogged down in thick mud, swamps, or snow where Russian tanks were far more suited to the terrain they fought in with 600mm (almost 24"). The Germans didn't even come close to recognizing the difference this made when tanks got bogged down 20km from an objective and the Russians had an entire extra half day to prepare themselves.

AND FINALLY, the Germans all around were just not ready for the infamous Russian winter. Vehicles wouldn't start, pistons would freeze to cylinder walls and destroy engines, soldiers didn't have proper winter clothing, vehicles had to either be left at idle or freeze solid overnight. It was atrocious. The amount of resources and causalities the Germans lost during the first winter wasn't the make or break deal for winning or losing the war, it just sped it up.

I think I covered all the big talking points but if you'd like me to expand on anything I'll see what I can do.

Most of this highlights the early war underestimates. There are more late war in 1943-45 that I am less familiar with.

Illius Willius covers a lot of the supply issues the German army had. To add and expand on a few of them another problem that the OKH anticipated but not fully appreciate was the problem that the wider railway gauge of the soviet railroads and extensive sabotage would prevent them from being able to be use the railways for weeks and sometimes months after capturing them. This put enormous strain on the capacity of the germans limited reserves of oil and supply trucks which would only become compounded with the onset of the raputista. The other major issue which lilius Willius address was the inferiority of the Panzer III and Panzer IV to the T-34. This was partially because as Illius Willius mentions the germans didn't know that the Russians were using the T-34 yet but also was because German Tanks in 1941 were not built primarily to fight other tanks as the germans preferred to use anti-tank guns when possible. As a result the Panzer III and IV were equipped with 57mm howitzers as there main cannon which were more useful in supporting infantry assaults but lacked the penetrating power of a 76 mm long-barreled cannon which was meant to pierce enemy armor at range. Moving beyond logistical considerations what the Wehrmacht mostly underestimated was the cohesiveness of the USSR, the number of tanks the red army possessed, and most crucially the number reserves it could muster. The German strategy was based on the belief that if it was able to destroy a sufficient portion of the Red Army that either the USSR would collapse due to the perceived widespread dislike for Stalin or at the very least would not be able to continue effective resistance. The Germans assumed that the Soviets would be able to raise 50 additional divisions to their pre existing 150 in the course of a 6 week campaign but in fact were able to raise 821 divisions in the course of six months something almost no one outside of Russia anticipated. The germans also destroyed more tanks in the first month than they believed the Russian possessed altogether. It was these sorts of intelligence failures that lead to the German defeat - sources Military History Visualized - Barbarossa the major errors and blunders David Glantz's Barbarossa Hitler's Invasion of Russia 1941 Andrew Robert's Storm of War