Continuity: When John Jameson and Mary Jane are walking down the stairs during John's celebration party, there are two people halfway down the staircase standing by themselves. When it does the closeup of John and Mary Jane, there are four people now standing in that spot.

Factual error: Harry stumbles onto his dad's secret room and it is free of dust except for a few cobwebs. While there may have been no human activity in the room for almost two years, there were holes in the room that let sunlight, air, and insects/arachnids in, therefore there must have been airflow. With the airflow, dust or dirt should have entered the room and collected on the items.

Continuity: In the first few shots of Mary Jane held hostage by Dr. Octopus in the factory, her arms above her head change from straight to bent and back.

Factual error: The only elevated trains in Manhattan are Metro North that goes to Connecticut and the N, Q, R, W line that goes to Brooklyn/Queens, and that line goes over a bridge. None of these trains are elevated in mid-Manhattan; and most certainly, the end of the subway line would not just be a big metal "bumper" that leads into the water.