Minor Plot hole: Captain America boards Red Skull's plane and notices that it contains several smaller suicide-bomber planes that are interestingly enough, painted with the name of the city they are each supposed to reach. You know, in case the devoted future dead pilots forget about where they need to explode.
But then, Captain America beats all the soldiers and Red Skull and somehow assumes that the plane is going to crash in New York City. This is a pretty big assumption to pull out of one's ass-hole. He saw that the plane had various targets across the United States, he saw that the bombs were not computer-guided but piloted by some Hydra's henchmen. How could he possibly think that it was going to crash or explode in New York without the pilots of the flying bombs ?
Minor Plot hole: Captain America's solution to the plane problem makes no sense. Why did he crash the plane in the Arctic ? Or if there was an auto-pilot on it, how could he crash it in the Arctic by simply using the joystick ? Was the auto-pilot selective in its prohibitions of directions ? Or were the screenwriters rushed to find a way to make Captain America freeze in the Arctic Sea ?
Major Plot hole: Captain America has a plan to defeat Red Skull ! He has to enter alone the military base – beat up as many Hydra Nazis as he can, then hope he will get captured by the hundreds of soldiers instead of being executed, then brought up to Red Skull himself in the exact room where his buddies will be ready to save him by crashing through the glass windows.
Ok. What if the glass windows were impervious to bullets ? What if Captain America was brought up in a different room of the colossal German base ? What if the soldiers simply killed Captain America while they were firing at him from all angles ? How can this be a good plan at all ? Captain America simply assumes things that are impossible to predict, or perhaps he just felt lucky.
Unaddressed Issue: In the 1940s, Johann Schmidt possesses a fake skin mask that is impossible to replicate even in the 2010s. Yes, the movie does have laser guns and tanks, but the technology became available only after Schmidt found the tesseract. This mask invention precedes it. How could it be so advanced ? It does not fit the time period.