Injuries are a part of being a superhero.  It's a matter of life and limb every time your superhero is called to action.  Injuries are a course of life.  Some injuries small as a scratch while leaping over a fence in pursuit of the bad guy, to taking a deadly hit from a superweapon are a scope of things to expect.
It's unlikely to see injuries every time a battle is fought, however, its unusual, and rather unrealistic (Even in such a realm as Super Powered Beings) to go unscathed for your entire life.
Playing off an injury can be a course of how a storyline evolves.  If Spiderman can't completely recover from Carnage's latest assault, Peter will have to find a way to explain his temporary disabilities to others.
Serious, life-threatening injuries have their place in all on-going RPs.  They help to develop stories and characters.  They can be a hindrance, in that your superhero may be out of action for however long it takes for them to be back on thier feet.  Determining that time, is up to the players and how you feel about keeping your character out of action, but within real time limits.  It also depends on the seriousness of the injury.
But as always, be logical enough that your partners arent left wondering if your superhero is being held to the same values as their own.