In first round try to dodge all attacks, running around the arena and waiting for enemy's mistake (notice that minions will flow in endlessly). Magneto will throw some bricks at you - avoid them for some time, then build a huge iron from the debris. Use it with Iron Man, so you can beat up the weakened villain.
Second round is quite the same - dodge enemy's attack, waiting for the proper quantity of the bricks to appear. After short time you will have an opportunity to build a pumpkin from them and hit it with Thor's hammer. Now you can smash Magneto.
The final round is very similar - wait for bricks, then build a battery from them and charge it with electricity. When it is done, switch into Spider-Man and shoot his web at the attachable point, so you can finally defeat an enemy.