In baseball, a hit or an error is determined by the circumstances of the play and whether the fielder was able to make a play on the ball. If a hard-hit ball is fielded cleanly by the second baseman but results in an injury, it would still typically be ruled a hit if the fielder did not successfully make an out.
However, if the ball goes through the fielder's legs or is misplayed in a way that is deemed to be purely a fielding error (for example, the fielder makes an obvious mistake), it could be ruled an error regardless of any injury incurred.
Ultimately, the official scorer decides based on the specifics of the play. If the fielder had a chance to make a play and failed to do so (while still being injured), it could be ruled an error. If the injury occurred after the ball had already passed and the fielder had no chance, it would likely be ruled a hit.