Logistics.

The campaign didn't start "late": the early summer months in Russia see significant rainfall, resulting in the so-called rasputitsa, literally "time without roads". Barbarossa's launch was timed so the ground could dry and the roads become usable again. In 1941 only 40,000 miles of the Soviet Union's 850,000 miles of road were hard-surfaced and suitable for use in all weathers. In the event, the roads were still atrociously bad. Most were little more than dirt tracks, which became rivers of glutinous mud after a summer downpour. These quickly became impassable quagmires to thousands of marching men, horses and vehicles. The roads were so bad that at one point it took the 7th Panzer Division two days to advance 90 kilometres. When they dried, they became rutted and treacherous, ready to turn an ankle or break an axle, and kicked up great clouds of dust that choked man, beast and machine alike: as well as being intolerable for men and horses, vehicles broke down at an alarming rate as filters were clogged and engines suffered dust contamination.

In such conditions, POL (Petrol, Oil, Lubricant) consumption accordingly rocketed: LVII Panzer Corps reported in August that its vehicles were consuming up to 30 litres of oil per 100 kilometres rather than the usual half-litre of oil. Even the few paved highways soon became unsuitable for large military movements because the ground they are built on was so poor: as early as two days into the campaign, XXXXVII Panzer Corps was delayed in crossing the Bug River because the surfaces of the approach roads were literally sinking into the sodden ground under such heavy weight of traffic.

Then there were the Germans' vehicles themselves: there was a critical shortage of trucks. The deficit was somewhat made up by thousands of captured French Army and requisitioned civilian vehicles, but these were very rarely 4-wheel drive models and were quickly ridden to destruction on the horrendous roads. Where there were no motor vehicles, horses were used: an infantry division had an establishment strength of 942 motor vehicles compared to 1,200 horses, while the Ostheer invaded the Soviet Union with a total of 625,000 horses. A horse cart is unlikely to travel more than thirty kilometres a day and no more than five kilometres in an hour, to say nothing of horses' vulnerability: they are easily incapacitated by colic caused by poor feeding, infections picked up from contaminated water, or severe cold. Within a year of Barbarossa being launched, fully half of the Ostheer's horses had perished.

The perception gained from looking at maps that the Ostheer nearly took Moscow conceals the fact that the offensive had reached its culminating point around Smolensk: the German logistic system was incapable of sustaining an advance more than 500 kilometres from railheads. After this point, it would have to stop and redress its lines of communications before it could hope to make the next bound. It tried to do this, but Stalin was in no mood to give the Germans the luxury of a pause and hammered their positions at Smolensk with relentless counteroffensives. There was no opportunity to tidy up supply lines because those very same supply lines had to supply troops desperately trying to fend off the counteroffensive. There was no particular tactical flaw that doomed Barbarossa (though many German Generals subsequently tried to blame Hitler for focusing on Kiev and the Ukraine before taking Moscow); it was flawed from the beginning owing to the impossibility of sustaining it.

Sources:

Robert Kirchubel, Operation Barbarossa: The German Invasion of Soviet Russia

Robert Kirchubel, Atlas of the Eastern Front

David Stahel, Operation Barbarossa and Germany's Defeat in the East