I am fairly well-read on Germany, so I can offer my own opinion on them, but as for Japan, all I really can say is Pearl Harbor?
Germany–
Stopping the bombing of Britain- British morale was in decline during the bombing, and despite what Axis and Allies represents, strategic bombing raids are pretty effective. With Britain being bombed, more Allied planes had to be focused on defense and less attacks on Germany. However, this mistake isn’t very severe, because Germany didn’t have the industrial capacity to match Britain plane for plane forever, especially with the UK’s colonies.
Calling off the attack on Moscow, which led to…
Capture of Leningrad, Stalingrad, and Moscow simultaneously- Huge mistake. Hitler, in his infinite wisdom, decided he needed three important cities, and that he had the capacity to take all three at the same time. The Germans were losing numerical superiority as more and more Russians from the far east were redeployed.
Stalingrad- Bombing the daylights out of the city created so much rubble that the Soviet troops could hide and fight an attrition war with the Germans. Without defined parameters, German tanks were easily stuck in what used to be streets and were easy prey for antitank weapons.
Inferior tank designs- The T-34 Soviet tank, while less manuverable and operated by inexperienced crews, was strong enough to resist shells of some German tank models completely. German tank crews were disheartened to find out in one incident, after they hit a T-34 and surrounded it, the surrendered Soviet crew was uninjured, just dazed from the impact, and the tank was fully operational. While this would be remedied with the Tiger tank, it was too late in the war.
At one point in the seige of Stalingrad, Hitler was so desperate to achieve victory he ordered experienced tank crews be armed with pistols and act as infantry. This cost the Germans immensley in terms of valuable soldiers.
The surrounding of the 6th army. Rather than place competent commanders, Hitler promoted those who followed orders, so when the 6th German army was counterattacked outside of Stalingrad, Field Marshal Paulus, rather than assemble a quick mechanized force of tanks and half-tracks which could have possibly repelled the disorganized Soviet attack, he patiently waited for orders from Fuhrer headquarters, which led to the defeat at Stalingrad.
The holocaust- so many resources were diverted into genocide rather than helping the Wehrmacht.
In general, Barbarossa was a huge mistake. Soviet industry was simply moved from the Ukraine and Belorussia to the Urals, and Soviet tank production was vastly superior to German tank production, something Hitler refused to believe.