"Now, as he lurched about in his efforts to muster all the strength he could for running he could hardly keep his eyes open; his thoughts became too slow for him to think of any other way of saving himself than running; he almost forgot that the walls were there for him to use although, here, they were concealed behind carefully carved furniture full of notches and protrusions - then, right beside him, lightly tossed, something flew down and rolled in front of him. It was an apple; then another one immediately flew at him; Gregor froze in shock; there was no longer any point in running as his father had decided to bombard him. He had filled his pockets with fruit from the bowl on the sideboard and now, without even taking the time for careful aim, threw one apple after another. These little, red apples rolled about on the floor, knocking into each other as if they had electric motors. An apple thrown without much force glanced against Gregor's back and slid off without doing any harm. Another one however, immediately following it, hit squarely and lodged in his back; Gregor wanted to drag himself away, as if he could remove the surprising, the incredible pain by changing his position; but he felt as if nailed to the spot and spread himself out, all his senses in confusion."
From this portion of the text, it is easier to tell how Gregor was injured. His father was on one of his rampages and took it out on Gregor. He started throwing food at his son, and an apple hit him squarely in the back. I see this symbolizing the disdain the family had for Gregor. The fact that it hit him in the back shows how they were unwilling to let him see that disdain clearly.