Because you stop searching when you find the bug.

You have to not execute

lines[] = Load(file.code);

bool bug_found = false;
i=0;
while(!bug_found)
{
  bug_found = findBug(lines[i]);
  //looks like I missed a bit, lemme fix
  if(bug_found)
  {
    break;
  }
  i++;
}
bug_fix(lines[i]);
// Who'd've thought that I'd need to fix a bug in a joke about fixing bugs
// Now that's some tasty irony ^-^'

You have to run

lines[] = Load(file.code);

def bugs[];
a = 0;
for(i=0;i<lines[].length();i++)
{
  if (findBug(lines[i])
  {
    bugs[a] = lines[i];
    a++;
  }
}
for(b=0;b<=a;b++)
{
  bug_fix(lines[b]);
}

/j