Continuity mistake: At one point near the beginning of the infiltration of the helicarriers, Captain America's chinstrap has a twist from his right jaw down to where it covers his chin. This is visible in two shots. The next time his right side is shown afterward, the twist is gone. The chinstrap is too tight for it to have flipped on its own accidentally, and the pad which covers his chin is molded so it wouldn't have sat properly on his face even if it had somehow flipped around. There were undoubtedly several prop helmets made, and this one must have been put together incorrectly.
Continuity mistake: After his last fight with Bucky Steve gets a few wounds on his face, which disappear when he comes out from the water.
Revealing mistake: When one of the guys is shooting the mini-gun at the overturned bus Captain America is in, the spent shells still have the bullets in them.
Continuity mistake: During the Nick Fury chase scene the amount of bullet holes and the damage change during the whole scene.
Other mistake: When Zola's algorithm is deployed and begins it shows the radius which barely reaches Staten Island, however it finds Tony Stark in NYC.
Suggested correction: The initial targeting radius shown at 1:53:27 is as you say. But the radius keeps growing. At 1:53:50, it is still growing and has almost reached Lake Ontario.
Suggested correction: It's possible certain people were pre-programmed in.
Factual error: When Cap, Falcon and Black Widow are being arrested after fighting the Winter Soldier in DC, a new helicopter shows up with a "K" call number, which are reserved for western stations. DC stations use "W" call numbers.
Continuity mistake: When Fury and Pierce are talking before the retinal scanner they are beside each other but in the next shot they are several feet apart.
Continuity mistake: When Bucky attacks Cap and the others on the freeway the sun is changing in every shot.